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- PDB-8oin: 55S mammalian mitochondrial ribosome with mtRF1 and P-site tRNA -

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Basic information

Entry
Database: PDB / ID: 8oin
Title55S mammalian mitochondrial ribosome with mtRF1 and P-site tRNA
Components
  • (28S ribosomal protein ...) x 8
  • (39S ribosomal protein ...) x 11
  • (Large ribosomal subunit protein ...) x 6
  • (Mitochondrial ribosomal protein ...) x 38
  • (Mitoribosomal protein ...) x 2
  • (Small ribosomal subunit protein ...) x 2
  • 12S rRNA
  • 16S rRNA
  • CP Phe-tRNA
  • Coiled-coil-helix-coiled-coil-helix domain containing 1
  • E-site tRNA
  • ICT1
  • Mrpl34
  • P-site Met-tRNA(fMet)
  • Peptide chain release factor 1, mitochondrial
  • Ribosomal protein
  • bL17m
  • mL42
  • mL44
  • mL54
  • mL62 (ICT1)
  • mL64
  • mRNA
  • mS23
  • mS39
  • uL16m
  • uL24m
  • uS9m
KeywordsRIBOSOME / mammalian mitochondrial ribosome / release factor mtRF1 / non-canonical stop codon
Function / homology
Function and homology information


Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / : / translation release factor activity / mitochondrial translational elongation / mitochondrial translational termination ...Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / : / translation release factor activity / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / translation release factor activity, codon specific / ribonuclease III activity / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / organelle membrane / ribosomal small subunit binding / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / double-stranded RNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / synapse / nucleolus / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Ribosomal protein L1, mitochondrial / Gonadotropin-releasing hormone / Gonadoliberin / Gonadotropin-releasing hormone / Gonadotropin-releasing hormones signature. / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Peptide chain release factor / PCRF domain / PCRF / Cysteine alpha-hairpin motif superfamily ...Ribosomal protein L1, mitochondrial / Gonadotropin-releasing hormone / Gonadoliberin / Gonadotropin-releasing hormone / Gonadotropin-releasing hormones signature. / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Peptide chain release factor / PCRF domain / PCRF / Cysteine alpha-hairpin motif superfamily / Peptide chain release factor class I superfamily / 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 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / 28S ribosomal protein S24, mitochondrial / Mitochondrial 28S ribosomal protein S34 / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S34 / Small ribosomal subunit protein uS5m, N-terminal / Prokaryotic-type class I peptide chain release factors signature. / 28S ribosomal protein S25, mitochondrial / Ribosomal protein L37, mitochondrial / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L55 / Pentatricopeptide repeat domain / Mitochondrial ribosomal protein L46 NUDIX / 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 L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Ribosomal protein L37/S30 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Mitochondrial ribosomal subunit protein / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / Ribosomal protein L35, mitochondrial / MRPL44, double-stranded RNA binding domain / Tim44-like domain / Tim44-like domain / Tim44 / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / Pentatricopeptide repeat / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / 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 / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / N-FORMYLMETHIONINE / GUANOSINE-5'-DIPHOSPHATE / : / PHENYLALANINE / SPERMIDINE / SPERMINE / : / RNA ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / N-FORMYLMETHIONINE / GUANOSINE-5'-DIPHOSPHATE / : / PHENYLALANINE / SPERMIDINE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12m / 28S ribosomal protein S14, mitochondrial / 28S ribosomal protein S18c, mitochondrial isoform 1 / Small ribosomal subunit protein mS25 / 28S ribosomal protein S28, mitochondrial / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL3m / Small ribosomal subunit protein uS7m / Mitochondrial ribosomal protein S11 / Large ribosomal subunit protein mL62 / 28S ribosomal protein S21, mitochondrial / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL28m / 39S ribosomal protein L20, mitochondrial isoform 1 / Large ribosomal subunit protein mL64 / Mitochondrial ribosomal protein L2 / Ribosomal protein / Mitochondrial ribosomal protein S23 / Large ribosomal subunit protein uL1m / Small ribosomal subunit protein uS15m / 28S ribosomal protein S24, mitochondrial / Mitochondrial ribosomal protein S22 / Mitochondrial ribosomal protein S34 / Progonadoliberin / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein uL14m / Mitochondrial ribosomal protein L57 / Large ribosomal subunit protein mL42 / 39S ribosomal protein L48, mitochondrial / Large ribosomal subunit protein uL23m / Small ribosomal subunit protein bS16m / 39S ribosomal protein S30, mitochondrial / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL22m / 39S ribosomal protein L27, mitochondrial / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L18 / Large ribosomal subunit protein bL35m / Mitochondrial ribosomal protein S27 / Large ribosomal subunit protein uL15m / Mitoribosomal protein bs6m, mrps6 / Large ribosomal subunit protein mL53 / Mitochondrial ribosomal protein L12 / Large ribosomal subunit protein uL30m / 39S ribosomal protein L41, mitochondrial / 28S ribosomal protein S17, mitochondrial / Large ribosomal subunit protein bL34m / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein mL51 / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Small ribosomal subunit protein mS31 / Large ribosomal subunit protein bL17m / Mitochondrial ribosomal protein S18A / Large ribosomal subunit protein uL11m / Small ribosomal subunit protein uS10m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL21m / 28S ribosomal protein S2, mitochondrial / Small ribosomal subunit protein mS33 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL52 / 28S ribosomal protein S35, mitochondrial isoform 1 / Large ribosomal subunit protein uL29m / Mitochondrial ribosomal protein L39 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL46 / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein uS5m / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein bL32m / 28S ribosomal protein S9, mitochondrial / Small ribosomal subunit protein mS39 / 39S ribosomal protein L13, mitochondrial / Peptide chain release factor 1, mitochondrial / Small ribosomal subunit protein mS40
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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.Cartn_x / _atom_site.Cartn_y ..._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_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_ptnr1_PDB_ins_code / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _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_db_accession / _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: Mitochondrial ribosomal protein L12
B2: Mitochondrial ribosomal protein L12
B3: Mitochondrial ribosomal protein L12
B4: Mitochondrial ribosomal protein L12
B5: Mitochondrial ribosomal protein L12
B6: Mitochondrial ribosomal protein L12
B7: E-site tRNA
B8: 16S rRNA
B9: CP Phe-tRNA
BA: Large ribosomal subunit protein uL22m
BB: 39S ribosomal protein L23, mitochondrial
BC: uL24m
BD: 39S ribosomal protein L27, mitochondrial
BE: Mitochondrial ribosomal protein L28
BF: Mitochondrial ribosomal protein L47
BG: Large ribosomal subunit protein uL30m
BH: Mitochondrial ribosomal protein L32
BI: Large ribosomal subunit protein bL33m
BJ: Large ribosomal subunit protein bL34m
BK: 39S ribosomal protein L35, mitochondrial
BL: Mitochondrial ribosomal protein L2
BM: ICT1
BN: Mitochondrial ribosomal protein L4
BO: Mitochondrial ribosomal protein L9
BP: Mitochondrial ribosomal protein L10
BQ: Mitochondrial ribosomal protein L11
BR: 39S ribosomal protein L13, mitochondrial
BS: Mitochondrial ribosomal protein L14
BT: 39S ribosomal protein L15, mitochondrial
BU: uL16m
BV: bL17m
BW: Mitochondrial ribosomal protein L18
BX: 39S ribosomal protein L19, mitochondrial
BY: Mitochondrial ribosomal protein L20
BZ: Mitochondrial ribosomal protein L21
Ba: 39S ribosomal protein L52, mitochondrial
Bb: Mitochondrial ribosomal protein L53
Bc: mL54
Bd: Mitochondrial ribosomal protein L55
Be: Mitochondrial ribosomal protein L57
Bf: mL62 (ICT1)
Bg: mL64
Bh: Mitochondrial ribosomal protein S18A
Bi: 39S ribosomal protein S30, mitochondrial
Bj: 39S ribosomal protein L1, mitochondrial
Bl: Ribosomal protein
Bm: Mitochondrial ribosomal protein L37
Bn: Mitochondrial ribosomal protein L38
Bo: Mitochondrial ribosomal protein L39
Bp: Mitochondrial ribosomal protein L40
Bq: 39S ribosomal protein L41, mitochondrial
Br: mL42
Bs: Large ribosomal subunit protein mL43
Bt: mL44
Bu: Mitochondrial ribosomal protein L45
Bv: Mitochondrial ribosomal protein L46
Bw: 39S ribosomal protein L48, mitochondrial
Bx: Mrpl34
By: Mitochondrial ribosomal protein L50
Bz: Large ribosomal subunit protein mL51
AA: 12S rRNA
AB: 28S ribosomal protein S35, mitochondrial isoform 1
AC: Mitochondrial ribosomal protein S24
AD: Small ribosomal subunit protein mS38
AE: Mitoribosomal protein bs6m, mrps6
AF: Mitochondrial ribosomal protein S7
AG: P-site Met-tRNA(fMet)
AH: Mitochondrial ribosomal protein S10
AI: mRNA
AJ: Mitochondrial ribosomal protein S12
AK: Mitochondrial ribosomal protein S14
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: Mitochondrial ribosomal protein S18C
AQ: 28S ribosomal protein S21, mitochondrial
AR: Mitochondrial ribosomal protein S22
AS: mS23
AT: Mitochondrial ribosomal protein S25
AU: Mitochondrial ribosomal protein S26
AV: Mitochondrial ribosomal protein S27
AW: Mitoribosomal protein ms28, mrps28
AX: Small ribosomal subunit protein mS29
AY: 28S ribosomal protein S31, mitochondrial
AZ: Mitochondrial ribosomal protein S33
Aa: Peptide chain release factor 1, mitochondrial
Ab: Mitochondrial ribosomal protein S2
Ac: Coiled-coil-helix-coiled-coil-helix domain containing 1
Ad: 28S ribosomal protein S5, mitochondrial isoform X2
Ae: mS39
Ag: uS9m
Ai: Mitochondrial ribosomal protein S11
Aj: Mitochondrial ribosomal protein S34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,212,795479
Polymers3,200,75994
Non-polymers12,036385
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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Mitochondrial ribosomal protein ... , 38 types, 43 molecules B1B2B3B4B5B6BEBFBHBLBNBOBPBQBSBWBYBZBbBdBeBhBmBnBoBpBuBvByAC...

#1: Protein
Mitochondrial ribosomal protein L12


Mass: 21268.975 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D0VGD9
#9: Protein Mitochondrial ribosomal protein L28


Mass: 30148.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZTW8
#10: Protein Mitochondrial ribosomal protein L47


Mass: 29894.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SGC7
#12: Protein Mitochondrial ribosomal protein L32


Mass: 23567.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3LTC4
#16: Protein Mitochondrial ribosomal protein L2


Mass: 33270.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287A143
#18: Protein Mitochondrial ribosomal protein L4


Mass: 33251.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287B9C4
#19: Protein Mitochondrial ribosomal protein L9


Mass: 30373.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3LR45
#20: Protein Mitochondrial ribosomal protein L10


Mass: 29238.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RWJ0
#21: Protein Mitochondrial ribosomal protein L11


Mass: 20809.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to NCBI reference sequence XP_003122536.1 (positions 17-192)
Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RU54
#23: Protein Mitochondrial ribosomal protein L14


Mass: 34796.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287BMZ6
#27: Protein Mitochondrial ribosomal protein L18


Mass: 21422.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to NCBI reference sequence XP_003121157.1 (positions 46-188)
Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A4X1VX01
#29: Protein Mitochondrial ribosomal protein L20


Mass: 17554.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZU56
#30: Protein Mitochondrial ribosomal protein L21


Mass: 23154.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RY70
#32: Protein Mitochondrial ribosomal protein L53


Mass: 12057.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_020942999.1 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D0LKT0
#34: Protein Mitochondrial ribosomal protein L55


Mass: 15156.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A4X1ULI6
#35: Protein Mitochondrial ribosomal protein L57


Mass: 12001.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287BP93
#38: Protein Mitochondrial ribosomal protein S18A


Mass: 22273.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to NCBI reference sequence XP_005654252.2 (positions 35-169)
Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RRH6
#42: Protein Mitochondrial ribosomal protein L37


Mass: 47917.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287BIV6
#43: Protein Mitochondrial ribosomal protein L38


Mass: 44656.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RW03
#44: Protein Mitochondrial ribosomal protein L39


Mass: 38523.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to NCBI reference sequence XP_003132793.4 (positions 30-324)
Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SHP6
#45: Protein Mitochondrial ribosomal protein L40


Mass: 19406.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZP98
#50: Protein Mitochondrial ribosomal protein L45


Mass: 35331.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3LGM5
#51: Protein Mitochondrial ribosomal protein L46


Mass: 32215.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SRT0
#54: Protein Mitochondrial ribosomal protein L50


Mass: 22785.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3L9H6
#58: Protein Mitochondrial ribosomal protein S24


Mass: 18935.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287ANU4
#61: Protein Mitochondrial ribosomal protein S7


Mass: 28150.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZJ25
#63: Protein Mitochondrial ribosomal protein S10


Mass: 23105.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RUU2
#65: Protein Mitochondrial ribosomal protein S12 / Mitoribosomal protein us12m / mrps12


Mass: 15257.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A0M3KL52
#66: Protein Mitochondrial ribosomal protein S14 / Mitoribosomal protein us14m / mrps14


Mass: 15120.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A0M3KL53
#71: Protein Mitochondrial ribosomal protein S18C / Mitoribosomal protein bs18m / mrps18c


Mass: 16211.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A0M3KL54
#73: Protein Mitochondrial ribosomal protein S22


Mass: 43234.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287AQT5
#75: Protein Mitochondrial ribosomal protein S25 / Mitoribosomal protein ms25 / mrps25


Mass: 19954.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A0M3KL55
#76: Protein Mitochondrial ribosomal protein S26


Mass: 23637.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287AY01
#77: Protein Mitochondrial ribosomal protein S27


Mass: 45761.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A5G2R1I0
#81: Protein Mitochondrial ribosomal protein S33


Mass: 16971.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1S8G3
#83: Protein Mitochondrial ribosomal protein S2


Mass: 31731.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1S001
#88: Protein Mitochondrial ribosomal protein S11


Mass: 20856.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZJJ6
#89: Protein Mitochondrial ribosomal protein S34


Mass: 55714.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287AVS9

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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 / Details: likely the CCA-end of a tRNA / Source: (natural) Sus scrofa (pig)
#3: RNA chain 16S rRNA


Mass: 504908.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to GenBan sequence ID NC_012095.1 (positions 1099-2669)
Source: (natural) Sus scrofa (pig)
#4: RNA chain CP Phe-tRNA


Mass: 23516.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver
#56: RNA chain 12S rRNA


Mass: 308452.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to NCBI reference sequence NC_012095.1 (positions 72-1031)
Source: (natural) Sus scrofa (pig)
#62: RNA chain P-site Met-tRNA(fMet)


Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Corresponds to GenBank sequence ID LC530718.1 (positions 1-71). In vitro transcribed human tRNA with formyl-methionine attached to the CCA-end of the tRNA.
Source: (synth.) Homo sapiens (human) / References: GenBank: 1208989970
#64: RNA chain mRNA


Mass: 2902.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic mRNA / Source: (synth.) Homo sapiens (human)

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Large ribosomal subunit protein ... , 6 types, 6 molecules BABGBIBJBsBz

#5: Protein Large ribosomal subunit protein uL22m / 39S ribosomal protein L22 / mitochondrial


Mass: 24313.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A4X1TXR4
#11: Protein Large ribosomal subunit protein uL30m / 39S ribosomal protein L30 / mitochondrial


Mass: 18921.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D0VJF4
#13: Protein Large ribosomal subunit protein bL33m / 39S ribosomal protein L33 / mitochondrial


Mass: 7508.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A4X1TLP9
#14: Protein Large ribosomal subunit protein bL34m / 39S ribosomal protein L34 / mitochondrial


Mass: 10871.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D1JE64
#48: Protein Large ribosomal subunit protein mL43


Mass: 17622.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1S8U4
#55: Protein Large ribosomal subunit protein mL51 / 39S ribosomal protein L51 / mitochondrial


Mass: 15249.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D1VKN8

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39S ribosomal protein ... , 11 types, 11 molecules BBBDBKBRBTBXBaBiBjBqBw

#6: Protein 39S ribosomal protein L23, mitochondrial


Mass: 17685.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A480JJI1
#8: Protein 39S ribosomal protein L27, mitochondrial / Mitochondrial ribosomal protein L27


Mass: 15943.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A4X1U0F6
#15: Protein 39S ribosomal protein L35, mitochondrial


Mass: 21548.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A5G2QZK0
#22: Protein 39S ribosomal protein L13, mitochondrial / Mitochondrial ribosomal protein L13


Mass: 22988.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: K7GP19
#24: Protein 39S ribosomal protein L15, mitochondrial


Mass: 33481.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A5G2RG26
#28: Protein 39S ribosomal protein L19, mitochondrial / Mitochondrial ribosomal protein L19


Mass: 34528.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3LNJ0
#31: Protein 39S ribosomal protein L52, mitochondrial


Mass: 17989.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1S9B7
#39: Protein 39S ribosomal protein S30, mitochondrial / Mitochondrial ribosomal protein S30


Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A480QIM3
#40: Protein 39S ribosomal protein L1, mitochondrial


Mass: 34372.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287AF82
#46: Protein 39S ribosomal protein L41, mitochondrial


Mass: 15073.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D1BPA5
#52: Protein 39S ribosomal protein L48, mitochondrial / 39S ribosomal protein L48 / mitochondrial isoform 1 / Mitochondrial ribosomal protein L48


Mass: 29942.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A480J9Z6

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Protein , 16 types, 16 molecules BCBMBUBVBcBfBgBlBrBtBxASAaAcAeAg

#7: Protein uL24m


Mass: 24893.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RHJ1
#17: Protein ICT1 / Mitochondrial ribosomal protein L3


Mass: 43708.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A140UHW4
#25: Protein uL16m


Mass: 28680.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: NP_001231896.1 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RI89
#26: Protein bL17m


Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RMQ4
#33: Protein mL54


Mass: 15957.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to NCBI reference sequence XP_003123104.1 (positions 55-183)
Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3LN63
#36: Protein mL62 (ICT1)


Mass: 23545.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZJR2
#37: Protein mL64


Mass: 25815.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZXA6
#41: Protein Ribosomal protein


Mass: 10841.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287A731
#47: Protein mL42


Mass: 16680.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287BQA1
#49: Protein mL44


Mass: 37527.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SR64
#53: Protein Mrpl34


Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to NCBI reference sequence NP_001231942.1 (positions 34-166)
Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A0R4J8D6
#74: Protein mS23


Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Corresponds to NCBI reference sequence XP_005669023.1 (positions 2-136)
Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287AEW3
#82: Protein Peptide chain release factor 1, mitochondrial / MRF-1 / MtRF-1


Mass: 55569.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human mitochondrial release factor 1 (mtRF1), with a C-terminal linker (GGSGGSG) 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 1


Mass: 13603.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SU49
#86: Protein mS39


Mass: 78518.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_005662461.1 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: K7GKS8
#87: Protein uS9m


Mass: 45604.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3LU08

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28S ribosomal protein ... , 8 types, 8 molecules ABALAMANAOAQAYAd

#57: Protein 28S ribosomal protein S35, mitochondrial isoform 1 / Mitochondrial ribosomal protein S35


Mass: 41357.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SG95
#67: Protein 28S ribosomal protein S15, mitochondrial


Mass: 29596.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287AKS1
#68: Protein 28S ribosomal protein S16, mitochondrial / Mitochondrial ribosomal protein S16


Mass: 15182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A480JTD7
#69: Protein 28S ribosomal protein S17, mitochondrial


Mass: 14452.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D1IXU1
#70: Protein 28S ribosomal protein S18b, mitochondrial / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2


Mass: 29220.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: Q767K8
#72: Protein 28S ribosomal protein S21, mitochondrial


Mass: 10724.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZNB3
#80: Protein 28S ribosomal protein S31, mitochondrial


Mass: 43516.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RME2
#85: Protein 28S ribosomal protein S5, mitochondrial isoform X2 / Mitochondrial ribosomal protein S5


Mass: 48213.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SU66

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Small ribosomal subunit protein ... , 2 types, 2 molecules ADAX

#59: Protein Small ribosomal subunit protein mS38


Mass: 22843.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D1P8R7
#79: Protein Small ribosomal subunit protein mS29


Mass: 46966.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D1XNL0

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Mitoribosomal protein ... , 2 types, 2 molecules AEAW

#60: Protein Mitoribosomal protein bs6m, mrps6


Mass: 14283.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A5K1V0G5
#78: Protein Mitoribosomal protein ms28, mrps28


Mass: 21014.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A0M3KL56

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Non-polymers , 11 types, 388 molecules

#90: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 332 / Source method: obtained synthetically / Formula: Mg
#91: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: K
#92: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#93: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#94: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#95: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#96: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#97: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#98: 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
#99: 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
#100: 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

-
Sample preparation

ComponentName: 55S mammalian mitochondrial ribosome with mtRF1 and P-site tRNA
Type: RIBOSOME
Details: Mammalian mitochondrial translation termination complex, in vitro reconstituted from porcine mitoribosomal subunits, human mtRF1-3xFLAG, human methionine-tRNA(formyl-methionine), and a ...Details: Mammalian mitochondrial translation termination complex, in vitro reconstituted from porcine mitoribosomal subunits, human mtRF1-3xFLAG, human methionine-tRNA(formyl-methionine), and a synthetic mRNA (5'-A AUG AGA CAA-3') containing the non-canonical stop codon AGA.
Entity ID: #1-#47, #49-#87, #89 / Source: NATURAL
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)Organism: Sus scrofa (pig) / Cellular location: Mitochondrial matrix / Organ: Liver / Organelle: Mitochondrion
Buffer solutionpH: 7.5
Details: 20mM HEPES-KOH pH=7.5, 100mM KCl, 20mM MgCl2, ~1% sucrose (from mtRF1 storage buffer)
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMpotassium chlorideKCl1
320 mMmagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: In vitro reconstituted complex.
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: 70 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 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6973
EM imaging opticsEnergyfilter slit width: 20 eV

-
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 live v4.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1471587
Details: Particles were picked with blob picker in Cryosparc live v4.
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50622 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeDetailsInitial refinement model-IDSource nameType
17NQH

7nqh

7NQHSus scrofa mitoribosome1PDBexperimental model
27QI4

7qi4

7QI4High-res mammalian mitoribosome2PDBexperimental model
3UniProt AF-O75570-F1mtRF1 model prediction3AlphaFoldin silico model

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