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- PDB-6gb2: Unique features of mammalian mitochondrial translation initiation... -

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Basic information

Entry
Database: PDB / ID: 6gb2
TitleUnique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 39S ribosomal subunit.
Components
  • ('Mitochondrial ribosomal protein ...) x 3
  • (Mitochondrial ribosomal protein ...) x 42
  • 16S ribosomal RNA, mitochondrial
  • CP tRNAPhe, mitochondrial
  • ICT1
  • Mrpl34
  • P-site fMet-tRNAMet, mitochondrial
  • Ribosomal protein
  • Translation initiation factor IF-2, mitochondrial
  • Uncharacterized protein
  • mL53, MRPL53
  • mL65, MRPS30
  • unassigned secondary structure elements
KeywordsRIBOSOME / translation initiation / initiation factor IF2 / mitochondria / membrane targeting
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / mitochondrial transcription / translation factor activity, RNA binding / mitochondrial translational termination / mitochondrial translational elongation / ribonuclease III activity / translation release factor activity, codon nonspecific / Mitochondrial translation initiation ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / mitochondrial transcription / translation factor activity, RNA binding / mitochondrial translational termination / mitochondrial translational elongation / ribonuclease III activity / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / ribosome disassembly / mitochondrial small ribosomal subunit / regulation of translational initiation / peptidyl-tRNA hydrolase activity / mitochondrial translation / organelle membrane / ribosomal small subunit binding / RNA processing / rescue of stalled ribosome / translation initiation factor activity / cell junction / large ribosomal subunit / double-stranded RNA binding / rRNA binding / nuclear body / ribosome / structural constituent of ribosome / protein domain specific binding / translation / ribonucleoprotein complex / nucleotide binding / GTPase activity / intracellular membrane-bounded organelle / mRNA binding / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / : ...Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L37, mitochondrial / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L28 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L35, mitochondrial / Ribosomal protein L51, mitochondrial / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Ribosomal protein L37/S30 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / : / : / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Ribosomal protein L7/L12, oligomerisation / 39S ribosomal protein L52, mitochondrial / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Mitoribosomal protein mL52 / : / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / MRPL44, double-stranded RNA binding domain / : / Ribosomal protein L7/L12 C-terminal domain / MRPL44 dsRNA-binding domain / Large ribosomal subunit protein mL44, endonuclease domain / : / Large ribosomal subunit protein bL9m C-terminal domain / Tim44-like domain / Tim44-like domain / Tim44 / : / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / 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, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / PEBP-like superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / : / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Beta-grasp domain superfamily / NTF2-like domain superfamily / NUDIX hydrolase-like domain superfamily / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / N-FORMYLMETHIONINE / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...GUANOSINE-5'-MONOPHOSPHATE / N-FORMYLMETHIONINE / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL62 / Mitochondrial ribosomal protein L18 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL28m / 39S ribosomal protein L20, mitochondrial isoform 1 / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein mL64 / 39S ribosomal protein L23, mitochondrial / Large ribosomal subunit protein bL34m / Ribosomal protein / Mitochondrial ribosomal protein L12 / Mitochondrial ribosomal protein L41 / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein mL37 / Mitochondrial ribosomal protein L57 / Large ribosomal subunit protein mL42 / 39S ribosomal protein L48, mitochondrial / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL22m / Mitochondrial ribosomal protein S18A / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / 39S ribosomal protein L27, mitochondrial / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL21m / Mitochondrial ribosomal protein L4 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein uL29m / Mitochondrial ribosomal protein L39 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein uL30m / 39S ribosomal protein L48, mitochondrial / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein mL50 / Mitochondrial ribosomal protein L55 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein bL9m / Translation initiation factor IF-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKummer, E. / Leibundgut, M. / Boehringer, D. / Ban, N.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
European Molecular Biology OrganizationALTF 1196-2014 Switzerland
Swiss National Science Foundation310030B_163478 Switzerland
Swiss National Science Foundation138262 Switzerland
CitationJournal: Nature / Year: 2018
Title: Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.
Authors: Eva Kummer / Marc Leibundgut / Oliver Rackham / Richard G Lee / Daniel Boehringer / Aleksandra Filipovska / Nenad Ban /
Abstract: Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation. The ...Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation. The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems. Mitochondrial translation initiation lacks initiation factor 1, which is essential in all other translation systems from bacteria to mammals. Furthermore, only one type of methionyl transfer RNA (tRNA) is used for both initiation and elongation, necessitating that the initiation factor specifically recognizes the formylated version of tRNA (fMet-tRNA). Lastly, most mitochondrial mRNAs do not possess 5' leader sequences to promote mRNA binding to the ribosome. There is currently little mechanistic insight into mammalian mitochondrial translation initiation, and it is not clear how mRNA engagement, initiator-tRNA recruitment and start-codon selection occur. Here we determine the cryo-EM structure of the complete translation initiation complex from mammalian mitochondria at 3.2 Å. We describe the function of an additional domain insertion that is present in the mammalian mitochondrial initiation factor 2 (mtIF2). By closing the decoding centre, this insertion stabilizes the binding of leaderless mRNAs and induces conformational changes in the rRNA nucleotides involved in decoding. We identify unique features of mtIF2 that are required for specific recognition of fMet-tRNA and regulation of its GTPase activity. Finally, we observe that the ribosomal tunnel in the initiating ribosome is blocked by insertion of the N-terminal portion of mitochondrial protein mL45, which becomes exposed as the ribosome switches to elongation mode and may have an additional role in targeting of mitochondrial ribosomes to the protein-conducting pore in the inner mitochondrial membrane.
History
DepositionApr 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
CL: Mitochondrial ribosomal protein L12
DL: Mitochondrial ribosomal protein L12
EL: Mitochondrial ribosomal protein L12
FL: Mitochondrial ribosomal protein L12
GL: Mitochondrial ribosomal protein L12
HL: Mitochondrial ribosomal protein L12
B0: Mitochondrial ribosomal protein L27
B1: Mitochondrial ribosomal protein L28
B2: Mitochondrial ribosomal protein L47
B3: 'Mitochondrial ribosomal protein L30
B4: 'Mitochondrial ribosomal protein L55
B5: Mitochondrial ribosomal protein L32
B6: Mitochondrial ribosomal protein L33
B7: Mitochondrial ribosomal protein L34
B8: Mitochondrial ribosomal protein L35
B9: Ribosomal protein
BA: 16S ribosomal RNA, mitochondrial
BB: CP tRNAPhe, mitochondrial
BC: Translation initiation factor IF-2, mitochondrial
BD: Mitochondrial ribosomal protein L2
BE: ICT1
BF: Mitochondrial ribosomal protein L4
BI: Mitochondrial ribosomal protein L9
BJ: Mitochondrial ribosomal protein L10
BK: Mitochondrial ribosomal protein L11
BL: Mitochondrial ribosomal protein L12
BN: Mitochondrial ribosomal protein L13
BO: Mitochondrial ribosomal protein L14
BP: Mitochondrial ribosomal protein L15
BQ: Mitochondrial ribosomal protein L16
BR: Mitochondrial ribosomal protein L17
BS: Mitochondrial ribosomal protein L18
BT: Mitochondrial ribosomal protein L19
BU: Mitochondrial ribosomal protein L20
BV: Mitochondrial ribosomal protein L21
BW: Mitochondrial ribosomal protein L22
BX: Mitochondrial ribosomal protein L23
BY: Mitochondrial ribosomal protein L24
Ba: Mitochondrial ribosomal protein L37
Bb: Mitochondrial ribosomal protein L38
Bc: Mitochondrial ribosomal protein L39
Bd: Mitochondrial ribosomal protein L40
Be: Mitochondrial ribosomal protein L41
Bf: Mitochondrial ribosomal protein L42
Bg: Mitochondrial ribosomal protein L43
Bh: Mitochondrial ribosomal protein L44
Bi: Mitochondrial ribosomal protein L45
Bj: Mitochondrial ribosomal protein L46
Bk: Mitochondrial ribosomal protein L48
Bl: Mrpl34
Bm: Mitochondrial ribosomal protein L50
Bn: Mitochondrial ribosomal protein L51
Bo: Mitochondrial ribosomal protein L52
Bp: mL53, MRPL53
Bq: Uncharacterized protein
Bt: Mitochondrial ribosomal protein L57
Bu: Mitochondrial ribosomal protein L58
Bv: 'Mitochondrial ribosomal protein L59
Bw: mL65, MRPS30
Bx: Mitochondrial ribosomal protein S18A
Bz: unassigned secondary structure elements
AV: P-site fMet-tRNAMet, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,993,750288
Polymers1,986,43362
Non-polymers7,317226
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area387750 Å2
ΔGint-4335 kcal/mol
Surface area580140 Å2
MethodPISA

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Components

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Mitochondrial ribosomal protein ... , 42 types, 48 molecules CLDLELFLGLHLBLB0B1B2B5B6B7B8BDBFBIBJBKBNBOBPBQBRBSBTBUBVBWBX...

#1: Protein
Mitochondrial ribosomal protein L12


Mass: 21268.975 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287ARV8
#2: Protein 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: F1RT79
#3: 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
#4: Protein Mitochondrial ribosomal protein L47


Mass: 30085.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1SGC7
#7: Protein Mitochondrial ribosomal protein L32 / bL32m


Mass: 21537.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver
#8: Protein Mitochondrial ribosomal protein L33


Mass: 7508.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZU68
#9: Protein Mitochondrial ribosomal protein L34


Mass: 10871.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287A119
#10: Protein Mitochondrial ribosomal protein L35


Mass: 21548.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SVC5
#15: 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) / References: UniProt: F1RRN2
#17: 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) / References: UniProt: A0A287B9C4, UniProt: F1S3J8*PLUS
#18: 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
#19: Protein Mitochondrial ribosomal protein L10


Mass: 29449.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWJ0
#20: Protein Mitochondrial ribosomal protein L11


Mass: 20809.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / References: UniProt: F1RU54
#21: Protein Mitochondrial ribosomal protein L13 / uL13m


Mass: 20633.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#22: Protein Mitochondrial ribosomal protein L14 / uL14m


Mass: 15955.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver
#23: Protein Mitochondrial ribosomal protein L15


Mass: 33481.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RSH0
#24: Protein Mitochondrial ribosomal protein L16


Mass: 28680.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RI89
#25: Protein Mitochondrial ribosomal protein L17


Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RMQ4
#26: Protein Mitochondrial ribosomal protein L18


Mass: 20582.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNK1
#27: Protein Mitochondrial ribosomal protein L19


Mass: 33441.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver
#28: 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
#29: 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
#30: Protein Mitochondrial ribosomal protein L22


Mass: 24313.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RQC9
#31: Protein Mitochondrial ribosomal protein L23


Mass: 17643.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZZC6
#32: Protein Mitochondrial ribosomal protein L24


Mass: 24893.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RHJ1
#33: 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) / References: UniProt: A0A287BIV6
#34: 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
#35: Protein Mitochondrial ribosomal protein L39


Mass: 38523.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SHP6
#36: Protein Mitochondrial ribosomal protein L40


Mass: 24075.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZP98
#37: Protein Mitochondrial ribosomal protein L41


Mass: 15073.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AWS0
#38: Protein Mitochondrial ribosomal protein L42


Mass: 16680.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287BQA1
#39: Protein Mitochondrial ribosomal protein L43


Mass: 17728.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S8U4
#40: Protein Mitochondrial ribosomal protein L44


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
#41: 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) / References: UniProt: I3LGM5
#42: 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) / References: UniProt: F1SRT0
#43: Protein Mitochondrial ribosomal protein L48


Mass: 23749.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1SUS9, UniProt: A0A480J9Z6*PLUS
#45: Protein Mitochondrial ribosomal protein L50


Mass: 18351.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3L9H6
#46: Protein Mitochondrial ribosomal protein L51


Mass: 15249.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287BE26
#47: Protein Mitochondrial ribosomal protein L52


Mass: 13813.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S9B7
#50: 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
#51: Protein Mitochondrial ribosomal protein L58


Mass: 23545.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZJR2
#54: Protein Mitochondrial ribosomal protein S18A


Mass: 22273.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRH6

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'Mitochondrial ribosomal protein ... , 3 types, 3 molecules B3B4Bv

#5: Protein 'Mitochondrial ribosomal protein L30


Mass: 18585.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1STE5
#6: 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) / References: UniProt: I3L9J0
#52: Protein 'Mitochondrial ribosomal protein L59


Mass: 25815.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZXA6

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Protein , 8 types, 8 molecules B9BCBEBlBpBqBwBz

#11: 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
#14: Protein Translation initiation factor IF-2, mitochondrial / IF2(mt)


Mass: 72811.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mitochondrial / Source: (gene. exp.) Homo sapiens (human) / Gene: MTIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P46199
#16: Protein ICT1 / Mitochondrial ribosomal protein L3


Mass: 38427.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#44: Protein Mrpl34


Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0R4J8D6
#48: Protein mL53, MRPL53


Mass: 12015.747 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver
#49: Protein Uncharacterized protein


Mass: 15957.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LN63
#53: Protein mL65, MRPS30


Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#55: Protein unassigned secondary structure elements


Mass: 5846.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned secondary structure elements have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver

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RNA chain , 3 types, 3 molecules BABBAV

#12: RNA chain 16S ribosomal RNA, mitochondrial


Mass: 504852.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 33320725
#13: RNA chain CP tRNAPhe, mitochondrial


Mass: 23402.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 76262549
#56: RNA chain P-site fMet-tRNAMet, mitochondrial


Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1208989970

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Non-polymers , 8 types, 228 molecules

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


Mass: 24.305 Da / Num. of mol.: 216 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#59: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#60: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#61: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S / Feature type: SUBJECT OF INVESTIGATION
#62: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#63: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S / Feature type: SUBJECT OF INVESTIGATION
#64: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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

Component
IDNameTypeEntity IDParent-IDSource
1mammalian mitochondrial translation initiation complexRIBOSOME#1-#560MULTIPLE SOURCES
2mammalian mitochondrial ribosomeRIBOSOME#1-#13, #15-#551NATURAL
3Translation initiation factor IF-2, mitochondrialCOMPLEX#141RECOMBINANT
4tRNACOMPLEX#561RECOMBINANT
Molecular weightValue: 2.85 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa (pig)9823
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24synthetic construct (others)32630
Buffer solutionpH: 7.6
SpecimenConc.: 0.171 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: contains 55S mitochondrial ribosome, mitochondrial initiation factor 2, mitochondrial formyl-Met-tRNAMet and MT-CO3 mRNA
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / 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
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 13936
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1EMAN1.9particle selection
4RELION2.1CTF correction
7Cootmodel fitting
8Omodel fitting
9UCSF Chimeramodel fitting
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
14RELION2.13D reconstruction
15PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1366787
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75666 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 56.9 / Protocol: OTHER / Space: RECIPROCAL

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