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- PDB-8oir: 55S human mitochondrial ribosome with mtRF1 and P-site tRNA -

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Basic information

Entry
Database: PDB / ID: 8oir
Title55S human mitochondrial ribosome with mtRF1 and P-site tRNA
Components
  • (28S ribosomal protein ...) x 27
  • (39S ribosomal protein ...) x 48
  • 12S rRNA
  • 16S rRNA
  • Aurora kinase A-interacting protein
  • CP Val-tRNA(Val)
  • Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
  • E-site tRNA
  • Growth arrest and DNA damage-inducible proteins-interacting protein 1
  • Large ribosomal subunit protein mL43
  • P-site Met-tRNA(Met)
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Peptide chain release factor 1, mitochondrial
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Ribosomal protein 63, mitochondrial
  • mRNA
KeywordsRIBOSOME / human mitochondrial ribosome / release factor mtRF1 / non-canonical stop codon
Function / homology
Function and homology information


rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / translation release factor activity, codon specific / mitochondrial translational elongation / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation ...rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / translation release factor activity, codon specific / mitochondrial translational elongation / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / mitochondrial translation / apoptotic mitochondrial changes / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / rescue of stalled cytosolic ribosome / Mitochondrial protein degradation / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / cell junction / regulation of translation / double-stranded RNA binding / ribosomal small subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / cell population proliferation / negative regulation of translation / mitochondrial inner membrane / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / intracellular membrane-bounded organelle / mRNA binding / apoptotic process / positive regulation of DNA-templated transcription / GTP binding / nucleolus / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, mitochondrial / : / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Peptide chain release factor / PCRF domain / PCRF / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 28S ribosomal protein S27, mitochondrial ...Ribosomal protein L1, mitochondrial / : / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Peptide chain release factor / PCRF domain / PCRF / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / : / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal protein S23 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / Mitochondrial 28S ribosomal protein S34 / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / : / Mitochondrial ribosome subunit S24 / Small ribosomal subunit protein uS5m, N-terminal / Small ribosomal subunit protein mS39, PPR / 28S ribosomal protein S25, mitochondrial / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Pentatricopeptide repeat domain / Mitochondrial ribosomal protein L48 / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L35, mitochondrial / Ribosomal protein S24/S35, mitochondrial, conserved domain / Ribosomal protein L51, mitochondrial / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit protein / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein L37/S30 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / : / : / Mitochondrial 28S ribosomal protein S30 (PDCD9) / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : / MRPL44, double-stranded RNA binding domain / : / MRPL44 dsRNA-binding domain / Large ribosomal subunit protein mL44, endonuclease domain / : / : / Large ribosomal subunit protein bL9m C-terminal domain / Large ribosomal subunit protein bL9m N-terminal domain / Tim44-like domain / Tim44-like domain / Pentatricopeptide (PPR) repeat profile. / Tim44 / : / : / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Ribosomal protein L46, N-terminal
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE-S-O HYBRID CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / METHIONINE / VALINE / : / : / : / RNA ...ADENOSINE-5'-TRIPHOSPHATE / FE-S-O HYBRID CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / METHIONINE / VALINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS14m / Large ribosomal subunit protein bL33m / Peptide chain release factor 1, mitochondrial / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein bL12m / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein uS9m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL55 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL64 / Large ribosomal subunit protein uL30m / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS31 / Large ribosomal subunit protein uL24m / Small ribosomal subunit protein mS37 / Large ribosomal subunit protein mL38 / Small ribosomal subunit protein uS3m / Large ribosomal subunit protein mL53 / Small ribosomal subunit protein mS39 / Large ribosomal subunit protein mL48 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL63 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL20m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein uL1m / Small ribosomal subunit protein mS26 / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL66 / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS2m / Large ribosomal subunit protein uL11m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein mS40 / Large ribosomal subunit protein mL42
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSaurer, M. / Leibundgut, M. / Scaiola, A. / Schoenhut, T. / Ban, N.
Funding support Switzerland, European Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation179190 Switzerland
Swiss National Science Foundation182341 Switzerland
European Molecular Biology Organization (EMBO)1074-2019European Union
CitationJournal: Science / Year: 2023
Title: Molecular basis of translation termination at noncanonical stop codons in human mitochondria.
Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / ...Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / David Gatfield / Aleksandra Filipovska / Nenad Ban /
Abstract: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the ...The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _em_3d_fitting_list.initial_refinement_model_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Apr 24, 2024Group: Data collection / Structure summary / Category: chem_comp / chem_comp_atom / chem_comp_bond
Item: _chem_comp.pdbx_synonyms / _chem_comp_atom.atom_id ..._chem_comp.pdbx_synonyms / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order
Revision 3.0Jun 26, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / em_admin / em_entity_assembly / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.pdbx_PDB_ins_code / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _em_admin.last_update / _em_entity_assembly.entity_id_list / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_seq_align_beg_ins_code / _struct_ref_seq.seq_align_beg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B1: 39S ribosomal protein L12, mitochondrial
B2: 39S ribosomal protein L12, mitochondrial
B3: 39S ribosomal protein L12, mitochondrial
B4: 39S ribosomal protein L12, mitochondrial
B5: 39S ribosomal protein L12, mitochondrial
B6: 39S ribosomal protein L12, mitochondrial
B7: E-site tRNA
B8: 16S rRNA
B9: CP Val-tRNA(Val)
BA: 39S ribosomal protein L22, mitochondrial
BB: 39S ribosomal protein L23, mitochondrial
BC: 39S ribosomal protein L24, mitochondrial
BD: 39S ribosomal protein L27, mitochondrial
BE: 39S ribosomal protein L28, mitochondrial
BF: 39S ribosomal protein L47, mitochondrial
BG: 39S ribosomal protein L30, mitochondrial
BH: 39S ribosomal protein L32, mitochondrial
BI: 39S ribosomal protein L33, mitochondrial
BJ: 39S ribosomal protein L34, mitochondrial
BK: 39S ribosomal protein L35, mitochondrial
BL: 39S ribosomal protein L2, mitochondrial
BM: 39S ribosomal protein L3, mitochondrial
BN: 39S ribosomal protein L4, mitochondrial
BO: 39S ribosomal protein L9, mitochondrial
BP: 39S ribosomal protein L10, mitochondrial
BQ: 39S ribosomal protein L11, mitochondrial
BR: 39S ribosomal protein L13, mitochondrial
BS: 39S ribosomal protein L14, mitochondrial
BT: 39S ribosomal protein L15, mitochondrial
BU: 39S ribosomal protein L16, mitochondrial
BV: 39S ribosomal protein L17, mitochondrial
BW: 39S ribosomal protein L18, mitochondrial
BX: 39S ribosomal protein L19, mitochondrial
BY: 39S ribosomal protein L20, mitochondrial
BZ: 39S ribosomal protein L21, mitochondrial
Ba: 39S ribosomal protein L52, mitochondrial
Bb: 39S ribosomal protein L53, mitochondrial
Bc: 39S ribosomal protein L54, mitochondrial
Bd: 39S ribosomal protein L55, mitochondrial
Be: Ribosomal protein 63, mitochondrial
Bf: Peptidyl-tRNA hydrolase ICT1, mitochondrial
Bg: Growth arrest and DNA damage-inducible proteins-interacting protein 1
Bh: 39S ribosomal protein S18a, mitochondrial
Bi: 39S ribosomal protein S30, mitochondrial
Bj: 39S ribosomal protein L1, mitochondrial
Bl: 39S ribosomal protein L36, mitochondrial
Bm: 39S ribosomal protein L37, mitochondrial
Bn: 39S ribosomal protein L38, mitochondrial
Bo: 39S ribosomal protein L39, mitochondrial
Bp: 39S ribosomal protein L40, mitochondrial
Bq: 39S ribosomal protein L41, mitochondrial
Br: 39S ribosomal protein L42, mitochondrial
Bs: Large ribosomal subunit protein mL43
Bt: 39S ribosomal protein L44, mitochondrial
Bu: 39S ribosomal protein L45, mitochondrial
Bv: 39S ribosomal protein L46, mitochondrial
Bw: 39S ribosomal protein L48, mitochondrial
Bx: 39S ribosomal protein L49, mitochondrial
By: 39S ribosomal protein L50, mitochondrial
Bz: 39S ribosomal protein L51, mitochondrial
AA: 12S rRNA
AB: 28S ribosomal protein S35, mitochondrial
AC: 28S ribosomal protein S24, mitochondrial
AD: Aurora kinase A-interacting protein
AE: 28S ribosomal protein S6, mitochondrial
AF: 28S ribosomal protein S7, mitochondrial
AG: P-site Met-tRNA(Met)
AH: 28S ribosomal protein S10, mitochondrial
AI: mRNA
AJ: 28S ribosomal protein S12, mitochondrial
AK: 28S ribosomal protein S14, mitochondrial
AL: 28S ribosomal protein S15, mitochondrial
AM: 28S ribosomal protein S16, mitochondrial
AN: 28S ribosomal protein S17, mitochondrial
AO: 28S ribosomal protein S18b, mitochondrial
AP: 28S ribosomal protein S18c, mitochondrial
AQ: 28S ribosomal protein S21, mitochondrial
AR: 28S ribosomal protein S22, mitochondrial
AS: 28S ribosomal protein S23, mitochondrial
AT: 28S ribosomal protein S25, mitochondrial
AU: 28S ribosomal protein S26, mitochondrial
AV: 28S ribosomal protein S27, mitochondrial
AW: 28S ribosomal protein S28, mitochondrial
AX: 28S ribosomal protein S29, mitochondrial
AY: 28S ribosomal protein S31, mitochondrial
AZ: 28S ribosomal protein S33, mitochondrial
Aa: Peptide chain release factor 1, mitochondrial
Ab: 28S ribosomal protein S2, mitochondrial
Ac: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
Ad: 28S ribosomal protein S5, mitochondrial
Ae: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Ag: 28S ribosomal protein S9, mitochondrial
Ai: 28S ribosomal protein S11, mitochondrial
Aj: 28S ribosomal protein S34, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,149,502509
Polymers3,136,48494
Non-polymers13,017415
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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39S ribosomal protein ... , 48 types, 53 molecules B1B2B3B4B5B6BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBX...

#1: Protein
39S ribosomal protein L12, mitochondrial / L12mt / MRP-L12 / 5c5-2 / Mitochondrial large ribosomal subunit protein bL12m


Mass: 21378.164 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P52815
#5: Protein 39S ribosomal protein L22, mitochondrial / L22mt / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / L25mt / MRP-L25 / Mitochondrial large ...L22mt / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / L25mt / MRP-L25 / Mitochondrial large ribosomal subunit protein uL22m


Mass: 23683.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NWU5
#6: Protein 39S ribosomal protein L23, mitochondrial / L23mt / MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein ...L23mt / MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / Ribosomal protein L23-like


Mass: 17849.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q16540
#7: Protein 39S ribosomal protein L24, mitochondrial / MRP-L24 / Mitochondrial large ribosomal subunit protein uL24m


Mass: 24953.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q96A35
#8: Protein 39S ribosomal protein L27, mitochondrial / MRP-L27 / Mitochondrial large ribosomal subunit protein bL27m


Mass: 16102.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9P0M9
#9: Protein 39S ribosomal protein L28, mitochondrial / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / ...MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / Mitochondrial large ribosomal subunit protein bL28m


Mass: 30202.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q13084
#10: Protein 39S ribosomal protein L47, mitochondrial / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis- ...MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis-related protein 1


Mass: 29508.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9HD33
#11: Protein 39S ribosomal protein L30, mitochondrial / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / MRP-L28 / Mitochondrial large ribosomal ...MRP-L30 / 39S ribosomal protein L28 / mitochondrial / MRP-L28 / Mitochondrial large ribosomal subunit protein uL30m


Mass: 18582.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q8TCC3
#12: Protein 39S ribosomal protein L32, mitochondrial / MRP-L32 / Mitochondrial large ribosomal subunit protein bL32m


Mass: 21437.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BYC8
#13: Protein 39S ribosomal protein L33, mitochondrial / MRP-L33 / Mitochondrial large ribosomal subunit protein bL33m


Mass: 7635.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: O75394
#14: Protein 39S ribosomal protein L34, mitochondrial / MRP-L34 / Mitochondrial large ribosomal subunit protein bL34m


Mass: 10183.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BQ48
#15: Protein 39S ribosomal protein L35, mitochondrial / MRP-L35 / Mitochondrial large ribosomal subunit protein bL35m


Mass: 21558.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NZE8
#16: Protein 39S ribosomal protein L2, mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit protein uL2m


Mass: 33355.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q5T653
#17: Protein 39S ribosomal protein L3, mitochondrial / MRP-L3 / Mitochondrial large ribosomal subunit protein uL3m


Mass: 38689.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P09001
#18: Protein 39S ribosomal protein L4, mitochondrial / MRP-L4 / Mitochondrial large ribosomal subunit protein uL4m


Mass: 34970.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BYD3
#19: Protein 39S ribosomal protein L9, mitochondrial / MRP-L9 / Mitochondrial large ribosomal subunit protein bL9m


Mass: 30296.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BYD2
#20: Protein 39S ribosomal protein L10, mitochondrial / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / MRP-L8 / Mitochondrial large ribosomal subunit ...MRP-L10 / 39S ribosomal protein L8 / mitochondrial / MRP-L8 / Mitochondrial large ribosomal subunit protein uL10m


Mass: 29322.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q7Z7H8
#21: Protein 39S ribosomal protein L11, mitochondrial / MRP-L11 / Mitochondrial large ribosomal subunit protein uL11m


Mass: 20716.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y3B7
#22: Protein 39S ribosomal protein L13, mitochondrial / L13mt / MRP-L13 / Mitochondrial large ribosomal subunit protein uL13m


Mass: 20765.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BYD1
#23: Protein 39S ribosomal protein L14, mitochondrial / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / MRP-L32 / Mitochondrial large ribosomal ...MRP-L14 / 39S ribosomal protein L32 / mitochondrial / MRP-L32 / Mitochondrial large ribosomal subunit protein uL14m


Mass: 15973.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q6P1L8
#24: Protein 39S ribosomal protein L15, mitochondrial / MRP-L15 / Mitochondrial large ribosomal subunit protein uL15m


Mass: 33473.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9P015
#25: Protein 39S ribosomal protein L16, mitochondrial / MRP-L16 / Mitochondrial large ribosomal subunit protein uL16m


Mass: 28496.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NX20
#26: Protein 39S ribosomal protein L17, mitochondrial / MRP-L17 / LYST-interacting protein 2 / Mitochondrial large ribosomal subunit protein bL17m


Mass: 20083.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NRX2
#27: Protein 39S ribosomal protein L18, mitochondrial / L18mt / MRP-L18 / Mitochondrial large ribosomal subunit protein uL18m


Mass: 20607.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9H0U6
#28: Protein 39S ribosomal protein L19, mitochondrial / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal ...MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal subunit protein bL19m


Mass: 33584.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P49406
#29: Protein 39S ribosomal protein L20, mitochondrial / MRP-L20 / Mitochondrial large ribosomal subunit protein bL20m


Mass: 17479.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BYC9
#30: Protein 39S ribosomal protein L21, mitochondrial / MRP-L21 / Mitochondrial large ribosomal subunit protein bL21m


Mass: 22847.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q7Z2W9
#31: Protein 39S ribosomal protein L52, mitochondrial / L52mt / MRP-L52 / Mitochondrial large ribosomal subunit protein mL52


Mass: 13682.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q86TS9
#32: Protein 39S ribosomal protein L53, mitochondrial / L53mt / MRP-L53 / Mitochondrial large ribosomal subunit protein mL53


Mass: 12167.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q96EL3
#33: Protein 39S ribosomal protein L54, mitochondrial / MRP-L54 / Mitochondrial large ribosomal subunit protein mL54


Mass: 15844.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q6P161
#34: Protein 39S ribosomal protein L55, mitochondrial / MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal ...MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal subunit protein mL55


Mass: 15160.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q7Z7F7
#38: Protein 39S ribosomal protein S18a, mitochondrial / S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / Mitochondrial large ribosomal ...S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / Mitochondrial large ribosomal subunit protein bS18a / Mitochondrial large ribosomal subunit protein mL66


Mass: 22224.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NVS2
#39: Protein 39S ribosomal protein S30, mitochondrial / S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ribosomal subunit ...S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ribosomal subunit protein mS30 / Programmed cell death protein 9


Mass: 50429.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NP92
#40: Protein 39S ribosomal protein L1, mitochondrial / L1mt / MRP-L1 / Mitochondrial large ribosomal subunit protein uL1m


Mass: 36967.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BYD6
#41: Protein 39S ribosomal protein L36, mitochondrial / MRP-L36 / BRCA1-interacting protein 1 / Mitochondrial large ribosomal subunit protein bL36m


Mass: 11809.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9P0J6
#42: Protein 39S ribosomal protein L37, mitochondrial / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit ...MRP-L37 / 39S ribosomal protein L2 / mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit protein mL37


Mass: 48183.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BZE1
#43: Protein 39S ribosomal protein L38, mitochondrial / MRP-L38 / Mitochondrial large ribosomal subunit protein mL38


Mass: 44659.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q96DV4
#44: Protein 39S ribosomal protein L39, mitochondrial / MRP-L39 / 39S ribosomal protein L5 / mitochondrial / MRP-L5 / Mitochondrial large ribosomal subunit ...MRP-L39 / 39S ribosomal protein L5 / mitochondrial / MRP-L5 / Mitochondrial large ribosomal subunit protein mL39


Mass: 38764.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NYK5
#45: Protein 39S ribosomal protein L40, mitochondrial / MRP-L40 / Mitochondrial large ribosomal subunit protein mL40 / Nuclear localization signal- ...MRP-L40 / Mitochondrial large ribosomal subunit protein mL40 / Nuclear localization signal-containing protein deleted in velocardiofacial syndrome / Up-regulated in metastasis


Mass: 24534.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NQ50
#46: Protein 39S ribosomal protein L41, mitochondrial / MRP-L41 / 39S ribosomal protein L27 homolog / Bcl-2-interacting mitochondrial ribosomal protein L41 ...MRP-L41 / 39S ribosomal protein L27 homolog / Bcl-2-interacting mitochondrial ribosomal protein L41 / Cell proliferation-inducing gene 3 protein / MRP-L27 homolog / Mitochondrial large ribosomal subunit protein mL41


Mass: 15404.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q8IXM3
#47: Protein 39S ribosomal protein L42, mitochondrial / MRP-L42 / 39S ribosomal protein L31 / mitochondrial / MRP-L31 / Mitochondrial large ribosomal ...MRP-L42 / 39S ribosomal protein L31 / mitochondrial / MRP-L31 / Mitochondrial large ribosomal subunit protein mL42


Mass: 16691.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y6G3
#49: Protein 39S ribosomal protein L44, mitochondrial / MRP-L44 / Mitochondrial large ribosomal subunit protein mL44


Mass: 37583.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA
References: UniProt: Q9H9J2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#50: Protein 39S ribosomal protein L45, mitochondrial / MRP-L45 / Mitochondrial large ribosomal subunit protein mL45


Mass: 35402.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BRJ2
#51: Protein 39S ribosomal protein L46, mitochondrial / MRP-L46 / Mitochondrial large ribosomal subunit protein mL46 / P2ECSL


Mass: 31748.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9H2W6
#52: Protein 39S ribosomal protein L48, mitochondrial / L48mt / MRP-L48 / Mitochondrial large ribosomal subunit protein mL48


Mass: 23970.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q96GC5
#53: Protein 39S ribosomal protein L49, mitochondrial / MRP-L49 / Mitochondrial large ribosomal subunit protein mL49 / Neighbor of FAU / NOF / Protein NOF1


Mass: 19225.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q13405
#54: Protein 39S ribosomal protein L50, mitochondrial / MRP-L50 / Mitochondrial large ribosomal subunit protein mL50


Mass: 18349.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q8N5N7
#55: Protein 39S ribosomal protein L51, mitochondrial / MRP-L51 / Mitochondrial large ribosomal subunit protein mL51 / bMRP-64 / bMRP64


Mass: 15125.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q4U2R6

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RNA chain , 6 types, 6 molecules B7B8B9AAAGAI

#2: RNA chain E-site tRNA


Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA
#3: RNA chain 16S rRNA


Mass: 500727.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NCBI Reference Sequence: NC_012920.1 added 3' GU (encoded on genome but not annotated as part of the 16S rRNA), N1437>U as in MT079070.1
Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: GenBank: 1563835895
#4: RNA chain CP Val-tRNA(Val)


Mass: 22989.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NCBI Reference Sequence: NC_012920.1 + aminoacylated CCA-end
Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: GenBank: NC_012920.1
#56: RNA chain 12S rRNA


Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NCBI Reference Sequence: NC_012920.1 + one C at 3'-end (encoded but not annotated as part of the sequence), a A103>G and A791>G as found in e.g. GenBank: OM714795.1
Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: GenBank: OM714795.1
#62: RNA chain P-site Met-tRNA(Met)


Mass: 22692.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NCBI Reference Sequence: NC_012920.1 + aminoacylated CCA-end
Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: GenBank: NC_012920.1
#64: RNA chain mRNA


Mass: 7329.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence as observed in the cryo-EM density map. / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA

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Protein , 8 types, 8 molecules BeBfBgBsADAaAcAe

#35: Protein Ribosomal protein 63, mitochondrial / hMRP63 / Mitochondrial large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / ...hMRP63 / Mitochondrial large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / Mitochondrial ribosomal protein L57


Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BQC6
#36: Protein Peptidyl-tRNA hydrolase ICT1, mitochondrial / 39S ribosomal protein L58 / mitochondrial / MRP-L58 / Digestion substraction 1 / DS-1 / Immature ...39S ribosomal protein L58 / mitochondrial / MRP-L58 / Digestion substraction 1 / DS-1 / Immature colon carcinoma transcript 1 protein / Mitochondrial large ribosomal subunit protein mL62


Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q14197, peptidyl-tRNA hydrolase
#37: Protein Growth arrest and DNA damage-inducible proteins-interacting protein 1 / 39S ribosomal protein L59 / mitochondrial / MRP-L59 / CKII beta-associating protein / CR6- ...39S ribosomal protein L59 / mitochondrial / MRP-L59 / CKII beta-associating protein / CR6-interacting factor 1 / CRIF1 / Mitochondrial large ribosomal subunit protein mL64 / Papillomavirus L2-interacting nuclear protein 1 / PLINP-1 / p53-responsive gene 6 protein


Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q8TAE8
#48: Protein Large ribosomal subunit protein mL43 / 39S ribosomal protein L43 / mitochondrial / L43mt / MRP-L43 / Mitochondrial ribosomal protein bMRP36a


Mass: 23352.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q8N983
#59: Protein Aurora kinase A-interacting protein / AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Mitochondrial ...AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Mitochondrial small ribosomal subunit protein mS38


Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9NWT8
#82: Protein Peptide chain release factor 1, mitochondrial / MRF-1 / MtRF-1


Mass: 56258.391 Da / Num. of mol.: 1 / Mutation: 311GGQ313 > AAQ
Source method: isolated from a genetically manipulated source
Details: Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) ...Details: Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) plasmid in HEK293 EBNA cells.
Source: (gene. exp.) Homo sapiens (human) / Gene: MTRF1 / Plasmid: pcDNA3.1(+) / Cell line (production host): HEK293 EBNA / Production host: Homo sapiens (human) / References: UniProt: O75570
#84: Protein Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S37 / mitochondrial / MRP-S37 / Mitochondrial small ribosomal subunit protein ...28S ribosomal protein S37 / mitochondrial / MRP-S37 / Mitochondrial small ribosomal subunit protein mS37 / Nuclear protein C2360


Mass: 13540.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q96BP2
#86: Protein Pentatricopeptide repeat domain-containing protein 3, mitochondrial / 28S ribosomal protein S39 / mitochondrial / MRP-S39 / Mitochondrial small ribosomal subunit protein ...28S ribosomal protein S39 / mitochondrial / MRP-S39 / Mitochondrial small ribosomal subunit protein mS39 / Transformation-related gene 15 protein / TRG-15


Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q96EY7

+
28S ribosomal protein ... , 27 types, 27 molecules ABACAEAFAHAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAbAdAgAiAj

#57: Protein 28S ribosomal protein S35, mitochondrial / MRP-S35 / S35mt / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt / Mitochondrial small ...MRP-S35 / S35mt / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt / Mitochondrial small ribosomal subunit protein mS35


Mass: 36898.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82673
#58: Protein 28S ribosomal protein S24, mitochondrial / MRP-S24 / S24mt / Mitochondrial small ribosomal subunit protein uS3m / bMRP-47 / bMRP47


Mass: 19046.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q96EL2
#60: Protein 28S ribosomal protein S6, mitochondrial / MRP-S6 / S6mt / Mitochondrial small ribosomal subunit protein bS6m


Mass: 14250.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82932
#61: Protein 28S ribosomal protein S7, mitochondrial / MRP-S7 / S7mt / Mitochondrial small ribosomal subunit protein uS7m / bMRP-27a / bMRP27a


Mass: 28186.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y2R9
#63: Protein 28S ribosomal protein S10, mitochondrial / MRP-S10 / S10mt / Mitochondrial small ribosomal subunit protein uS10m


Mass: 23033.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82664
#65: Protein 28S ribosomal protein S12, mitochondrial / MRP-S12 / S12mt / MT-RPS12 / Mitochondrial small ribosomal subunit protein uS12m


Mass: 15200.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: O15235
#66: Protein 28S ribosomal protein S14, mitochondrial / MRP-S14 / S14mt / Mitochondrial small ribosomal subunit protein uS14m


Mass: 15168.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: O60783
#67: Protein 28S ribosomal protein S15, mitochondrial / MRP-S15 / S15mt / Mitochondrial small ribosomal subunit protein uS15m


Mass: 29903.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82914
#68: Protein 28S ribosomal protein S16, mitochondrial / MRP-S16 / S16mt / Mitochondrial small ribosomal subunit protein bS16m


Mass: 15371.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y3D3
#69: Protein 28S ribosomal protein S17, mitochondrial / MRP-S17 / S17mt / Mitochondrial small ribosomal subunit protein uS17m


Mass: 14526.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y2R5
#70: Protein 28S ribosomal protein S18b, mitochondrial / MRP-S18-b / Mrps18-b / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2 / ...MRP-S18-b / Mrps18-b / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2 / Mitochondrial small ribosomal subunit protein bS18b / Mitochondrial small ribosomal subunit protein mS40


Mass: 29440.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y676
#71: Protein 28S ribosomal protein S18c, mitochondrial / MRP-S18-c / Mrps18-c / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1 / ...MRP-S18-c / Mrps18-c / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1 / Mitochondrial small ribosomal subunit protein bS18c / Mitochondrial small ribosomal subunit protein bS18m


Mass: 15876.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y3D5
#72: Protein 28S ribosomal protein S21, mitochondrial / MRP-S21 / S21mt / Mitochondrial small ribosomal subunit protein bS21m


Mass: 10806.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GenBank: AAH04566.2 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82921
#73: Protein 28S ribosomal protein S22, mitochondrial / MRP-S22 / S22mt / Mitochondrial small ribosomal subunit protein mS22


Mass: 41337.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82650
#74: Protein 28S ribosomal protein S23, mitochondrial / MRP-S23 / S23mt / Mitochondrial small ribosomal subunit protein mS23


Mass: 21805.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y3D9
#75: Protein 28S ribosomal protein S25, mitochondrial / MRP-S25 / S25mt / Mitochondrial small ribosomal subunit protein mS25


Mass: 20146.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82663
#76: Protein 28S ribosomal protein S26, mitochondrial / MRP-S26 / S26mt / 28S ribosomal protein S13 / mitochondrial / MRP-S13 / S13mt / Mitochondrial small ...MRP-S26 / S26mt / 28S ribosomal protein S13 / mitochondrial / MRP-S13 / S13mt / Mitochondrial small ribosomal subunit protein mS26


Mass: 24259.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9BYN8
#77: Protein 28S ribosomal protein S27, mitochondrial / MRP-S27 / S27mt / Mitochondrial ribosomal protein S27 / Mitochondrial small ribosomal subunit protein mS27


Mass: 47669.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q92552
#78: Protein 28S ribosomal protein S28, mitochondrial / MRP-S28 / S28mt / 28S ribosomal protein S35 / mitochondrial / MRP-S35 / S35mt / Mitochondrial small ...MRP-S28 / S28mt / 28S ribosomal protein S35 / mitochondrial / MRP-S35 / S35mt / Mitochondrial small ribosomal subunit protein bS1m


Mass: 20878.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y2Q9
#79: Protein 28S ribosomal protein S29, mitochondrial / MRP-S29 / S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring ...MRP-S29 / S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring protein / Mitochondrial small ribosomal subunit protein mS29


Mass: 45634.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P51398
#80: Protein 28S ribosomal protein S31, mitochondrial / MRP-S31 / S31mt / Imogen 38 / Mitochondrial small ribosomal subunit protein mS31


Mass: 45391.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q92665
#81: Protein 28S ribosomal protein S33, mitochondrial / MRP-S33 / S33mt / Mitochondrial small ribosomal subunit protein mS33


Mass: 12657.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y291
#83: Protein 28S ribosomal protein S2, mitochondrial / MRP-S2 / S2mt / Mitochondrial small ribosomal subunit protein uS2m


Mass: 33298.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q9Y399
#85: Protein 28S ribosomal protein S5, mitochondrial / MRP-S5 / S5mt / Mitochondrial small ribosomal subunit protein uS5m


Mass: 48094.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82675
#87: Protein 28S ribosomal protein S9, mitochondrial / MRP-S9 / S9mt / Mitochondrial small ribosomal subunit protein uS9m


Mass: 45909.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82933
#88: Protein 28S ribosomal protein S11, mitochondrial / MRP-S11 / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2 / Mitochondrial small ribosomal ...MRP-S11 / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2 / Mitochondrial small ribosomal subunit protein uS11m


Mass: 20663.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82912
#89: Protein 28S ribosomal protein S34, mitochondrial / S34mt / Mitochondrial small ribosomal subunit protein mS34


Mass: 25695.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82930

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Non-polymers , 9 types, 418 molecules

#90: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: K
#91: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 354 / Source method: obtained synthetically / Formula: Mg
#92: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#93: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#94: Chemical ChemComp-FS2 / FE-S-O HYBRID CLUSTER


Mass: 335.508 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4O3S2
#95: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#96: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#97: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#98: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 55S human mitochondrial ribosome with mtRF1 and P-site tRNA
Type: RIBOSOME
Details: 55S human mitochondrial ribosome in complex with mtRF1(AAQ)-3xFLAG, human methionine-tRNA(Met), and an mRNA containing a non-canonical stop codon, purified from HEK293 EBNA cells.
Entity ID: #1-#47, #49-#89 / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
112.6 MDaNO
211.5 MDaNO
311.0 MDaNO
410.03 MDaNO
510.05 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDCellular locationOrganelle
21Homo sapiens (human)9606Mitochondrial matrixMitochondrion
41Homo sapiens (human)9606Mitochondrial matrixMitochondrion
51Homo sapiens (human)9606Mitochondrial matrixMitochondria
61Homo sapiens (human)9606Mitochondrial matrixMitochondrion
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293 EBNA / Cell: HEK293 EBNA / Plasmid: pcDNA3.1(+)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMpotassium chlorideKCl1
320 mMmagnesium chlorideMgCl21
41 mMDTTHSCH2CH(OH)CH(OH)CH2SH1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Affinity-purified 55S mitoribosome.
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 43882
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
4cryoSPARC4CTF correction
7Coot0.9.8.4model fitting
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
12cryoSPARC43D reconstruction
13PHENIX1.20.1model refinement
Image processingDetails: Micrographs were motion corrected and CTF parameters were estimated using Cryosparc.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5423665
Details: Particles were picked with blob picker in Cryosparc.
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41288 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeDetailsInitial refinement model-IDSource nameType
17QI4

7qi4

7QI4High-res mammalian mitoribosome1PDBexperimental model
2UniProt AF-O75570-F1human mtRF1 model prediction2AlphaFoldin silico model

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