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- PDB-7nsi: 55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E) -

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Basic information

Entry
Database: PDB / ID: 7nsi
Title55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E)
Components
  • (28S ribosomal protein ...) x 16
  • (39S ribosomal protein ...) x 33
  • (Mitochondrial ribosomal protein ...) x 17
  • 12S rRNA
  • 16S rRNA
  • Aurora kinase A interacting protein 1
  • CP tRNAPhe
  • Coiled-coil-helix-coiled-coil-helix domain containing 1
  • Death associated protein 3
  • ICT1
  • Interferon alpha-inducible protein 6
  • Mitoribosomal protein us12m, mrps12
  • Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,mS39,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3
  • Ribosomal protein
  • Ribosomal_L2_C domain-containing protein
  • Ribosome-recycling factor, mitochondrial
  • TGS domain-containing protein
  • bL32m
  • mL42
  • mL53
  • mRNA
  • tRNA (P/E)
  • uL14m
  • uS17m
  • unknown
KeywordsTRANSLATION / Ribosome / Mitochondria / mtRRF / Recycling
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific ...Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation termination / Mitochondrial protein degradation / ribosome disassembly / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / organelle membrane / positive regulation of proteolysis / ribosomal small subunit binding / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / double-stranded RNA binding / ribosome biogenesis / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / synapse / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 ...Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif 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 / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / 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 / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S24/S35, mitochondrial, conserved domain / Ribosomal protein S30, mitochondrial / Mitochondrial ribosomal subunit protein / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / 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) / 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 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 / Pentatricopeptide repeat / Ribosomal protein L49/IMG2 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial large subunit ribosomal protein (Img2) / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / 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 / 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 / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile.
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 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 / 39S ribosomal protein L18, mitochondrial isoform 1 / 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 bL28m / 39S ribosomal protein L20, mitochondrial isoform 1 / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein mL64 / Large ribosomal subunit protein bL34m / Mitochondrial ribosomal protein L2 / 28S ribosomal protein S24, mitochondrial / Mitochondrial ribosomal protein S22 / Mitochondrial ribosomal protein L12 / Mitochondrial ribosomal protein S34 / Mitochondrial ribosomal protein L41 / Mitochondrial ribosomal protein L4 / Small ribosomal subunit protein mS38 / 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 uL23m / Small ribosomal subunit protein bS16m / 39S ribosomal protein L11, mitochondrial isoform a / 39S ribosomal protein L16, mitochondrial / 39S ribosomal protein L54, mitochondrial / 39S ribosomal protein S30, mitochondrial / 39S ribosomal protein L10, mitochondrial isoform a / 28S ribosomal protein S31, mitochondrial / Ribosomal protein / TGS domain-containing protein / 39S ribosomal protein L49, mitochondrial / Uncharacterized protein / 28S ribosomal protein S15, mitochondrial / Mitochondrial ribosomal protein S18A / Large ribosomal subunit protein mL40 / Mitochondrial ribosomal protein S27 / Large ribosomal subunit protein uL15m / Mitochondrial ribosomal protein S23 / Large ribosomal subunit protein uL24m / Mitochondrial ribosomal protein S17 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL22m / 39S ribosomal protein L27, mitochondrial / Small ribosomal subunit protein uS10m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein bL21m / 28S ribosomal protein S2, mitochondrial / Small ribosomal subunit protein mS26 / 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 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein uL30m / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein uS5m / Pentatricopeptide repeat domain 3 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein mL50 / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein S6 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL9m / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein bL32m / 28S ribosomal protein S9, mitochondrial / 39S ribosomal protein L13, mitochondrial / Small ribosomal subunit protein mS40 / Ribosome-recycling factor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsKummer, E. / Schubert, K. / Ban, N.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO) Switzerland
Swiss National Science Foundation Switzerland
CitationJournal: Mol Cell / Year: 2021
Title: Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.
Authors: Eva Kummer / Katharina Noel Schubert / Tanja Schoenhut / Alain Scaiola / Nenad Ban /
Abstract: The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as ...The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.
History
DepositionMar 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-12568
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Structure viewerMolecule:
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Assembly

Deposited unit
B0: 39S ribosomal protein L27, mitochondrial
B1: 39S ribosomal protein L28, mitochondrial
B2: Mitochondrial ribosomal protein L47
B3: 39S ribosomal protein L30, mitochondrial
B4: Mitochondrial ribosomal protein L55
B5: bL32m
B6: 39S ribosomal protein L33, mitochondrial
BB: CP tRNAPhe
B7: 39S ribosomal protein L34, mitochondrial
BD: Ribosomal_L2_C domain-containing protein
BE: ICT1
BF: Mitochondrial ribosomal protein L4
BG: Ribosome-recycling factor, mitochondrial
BI: 39S ribosomal protein L9, mitochondrial
BJ: 39S ribosomal protein L10, mitochondrial isoform a
BK: 39S ribosomal protein L11, mitochondrial isoform a
BN: 39S ribosomal protein L13, mitochondrial
BO: uL14m
BP: 39S ribosomal protein L15, mitochondrial
BQ: 39S ribosomal protein L16, mitochondrial
BR: 39S ribosomal protein L17, mitochondrial
BS: 39S ribosomal protein L18, mitochondrial isoform 1
BT: 39S ribosomal protein L19, mitochondrial
BU: 39S ribosomal protein L20, mitochondrial isoform 1
BV: 39S ribosomal protein L21, mitochondrial isoform d
BW: 39S ribosomal protein L22, mitochondrial
BX: 39S ribosomal protein L23, mitochondrial
BY: 39S ribosomal protein L24, mitochondrial isoform X1
Ba: 39S ribosomal protein L37, mitochondrial
Bb: 39S ribosomal protein L38, mitochondrial
Bc: TGS domain-containing protein
Bd: Mitochondrial ribosomal protein L40
Be: Mitochondrial ribosomal protein L41
Bf: mL42
Bg: 39S ribosomal protein L43, mitochondrial isoform X2
B8: 39S ribosomal protein L35, mitochondrial
Bh: 39S ribosomal protein L44, mitochondrial
Bi: Mitochondrial ribosomal protein L45
Bj: 39S ribosomal protein L46, mitochondrial
Bk: 39S ribosomal protein L48, mitochondrial
Bl: 39S ribosomal protein L49, mitochondrial
Bm: 39S ribosomal protein L50, mitochondrial
Bn: 39S ribosomal protein L51, mitochondrial
Bo: 39S ribosomal protein L52, mitochondrial
Bp: mL53
Bq: 39S ribosomal protein L54, mitochondrial
Bt: Mitochondrial ribosomal protein L57
Bu: Mitochondrial ribosomal protein L58
Bv: 39S ribosomal protein L59, mitochondrial
Bw: 39S ribosomal protein S30, mitochondrial
Bx: Mitochondrial ribosomal protein S18A
AA: 12S rRNA
B9: Ribosomal protein
AV: tRNA (P/E)
AX: mRNA
BA: 16S rRNA
AB: 28S ribosomal protein S2, mitochondrial
AC: 28S ribosomal protein S24, mitochondrial
AE: 28S ribosomal protein S5, mitochondrial isoform X2
AF: Mitochondrial ribosomal protein S6
AG: 28S ribosomal protein S7, mitochondrial
AI: 28S ribosomal protein S9, mitochondrial
AJ: 28S ribosomal protein S10, mitochondrial
AK: Mitochondrial ribosomal protein S11
AL: Mitoribosomal protein us12m, mrps12
AN: 28S ribosomal protein S14, mitochondrial
AO: 28S ribosomal protein S15, mitochondrial
AP: 28S ribosomal protein S16, mitochondrial
AQ: uS17m
AR: 28S ribosomal protein S18c, mitochondrial isoform 1
AU: 28S ribosomal protein S21, mitochondrial
AZ: unknown
Aa: Mitochondrial ribosomal protein S22
Ab: Mitochondrial ribosomal protein S23
Ac: Interferon alpha-inducible protein 6
Ad: 28S ribosomal protein S26, mitochondrial
Ae: Mitochondrial ribosomal protein S27
Af: 28S ribosomal protein S28, mitochondrial
Ag: Death associated protein 3
Ah: 28S ribosomal protein S31, mitochondrial
Ai: Mitochondrial ribosomal protein S33
Aj: Mitochondrial ribosomal protein S34
Ak: 28S ribosomal protein S35, mitochondrial isoform 1
Am: Coiled-coil-helix-coiled-coil-helix domain containing 1
An: Aurora kinase A interacting protein 1
Ao: Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,mS39,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3
Ap: 28S ribosomal protein S18b, mitochondrial
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,103,770431
Polymers3,093,93793
Non-polymers9,834338
Water543
1


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

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Components

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39S ribosomal protein ... , 33 types, 33 molecules B0B1B3B6B7BIBJBKBNBPBQBRBSBTBUBVBWBXBYBaBbBgB8BhBjBkBlBmBnBo...

#1: 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) / References: UniProt: F1RT79
#2: Protein 39S ribosomal protein L28, mitochondrial


Mass: 30148.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZTW8
#4: Protein 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) / References: UniProt: F1STE5
#7: Protein 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) / References: UniProt: A0A286ZU68
#9: Protein 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) / References: UniProt: A0A287A119
#14: Protein 39S ribosomal protein L9, mitochondrial


Mass: 30373.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LR45
#15: Protein 39S ribosomal protein L10, mitochondrial isoform a


Mass: 29449.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480VPY3
#16: Protein 39S ribosomal protein L11, mitochondrial isoform a


Mass: 20809.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480KRD0
#17: Protein 39S ribosomal protein L13, mitochondrial / Mitochondrial ribosomal protein L13


Mass: 20633.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GP19
#19: 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) / References: UniProt: A0A5G2RG26
#20: Protein 39S ribosomal protein L16, mitochondrial


Mass: 28680.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480MAF3
#21: Protein 39S ribosomal protein L17, mitochondrial


Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RMQ4
#22: Protein 39S ribosomal protein L18, mitochondrial isoform 1 / ICT1 / 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: A0A0R4J8D5
#23: Protein 39S ribosomal protein L19, mitochondrial / Mitochondrial ribosomal protein L19


Mass: 33441.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LNJ0
#24: Protein 39S ribosomal protein L20, mitochondrial isoform 1 / Mitochondrial ribosomal protein L20


Mass: 17554.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZU56
#25: Protein 39S ribosomal protein L21, mitochondrial isoform d


Mass: 23154.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RY70
#26: Protein 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) / References: UniProt: F1RQC9
#27: Protein 39S ribosomal protein L23, mitochondrial


Mass: 17643.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JJI1
#28: Protein 39S ribosomal protein L24, mitochondrial isoform X1 / 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
#29: Protein 39S ribosomal protein L37, mitochondrial / 39S ribosomal protein L37 / mitochondrial isoform 2 / 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
#30: Protein 39S ribosomal protein L38, mitochondrial / Mitochondrial ribosomal protein L38


Mass: 44656.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RW03
#35: Protein 39S ribosomal protein L43, mitochondrial isoform X2 / 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
#36: 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) / References: UniProt: F1SVC5
#37: Protein 39S ribosomal protein L44, mitochondrial / Mitochondrial ribosomal protein L44


Mass: 37527.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SR64
#39: Protein 39S ribosomal protein L46, mitochondrial


Mass: 32215.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SRT0
#40: 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) / References: UniProt: A0A480J9Z6
#41: Protein 39S ribosomal protein L49, mitochondrial


Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1V1G7
#42: Protein 39S ribosomal protein L50, mitochondrial


Mass: 22785.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L9H6
#43: Protein 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) / References: UniProt: A0A287BE26
#44: Protein 39S ribosomal protein L52, mitochondrial


Mass: 13813.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S9B7
#46: Protein 39S ribosomal protein L54, mitochondrial


Mass: 15957.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480PHA9
#49: Protein 39S ribosomal protein L59, mitochondrial / Growth arrest and DNA damage-inducible proteins-interacting protein 1


Mass: 25815.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZXA6
#50: 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) / References: UniProt: A0A480QIM3

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Mitochondrial ribosomal protein ... , 17 types, 22 molecules B2B4BFBdBeBiBtBuBxAFAKAaAbAeAiAjCLDLELFLGLHL

#3: 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) / References: UniProt: F1SGC7
#5: 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
#12: 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: A0A287B2W3
#32: 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: A0A5G2R2V2
#33: 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 L45


Mass: 35331.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM5
#47: 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) / References: UniProt: A0A287BP93
#48: Protein Mitochondrial ribosomal protein L58 / Peptidyl-tRNA hydrolase ICT1 / mitochondrial / mitochondrial isoform 1


Mass: 23545.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJR2
#51: 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: A0A5G2R1G5
#60: Protein Mitochondrial ribosomal protein S6


Mass: 30365.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LEJ9
#64: Protein Mitochondrial ribosomal protein S11


Mass: 20841.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJJ6
#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) / References: UniProt: A0A287AQT5
#74: Protein Mitochondrial ribosomal protein S23


Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2RMZ2
#77: Protein Mitochondrial ribosomal protein S27


Mass: 51945.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2R5D6
#81: Protein Mitochondrial ribosomal protein S33


Mass: 12544.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S8G3
#82: Protein Mitochondrial ribosomal protein S34


Mass: 25843.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AVS9
#88: 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) / References: UniProt: A0A287ARV8

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Protein , 16 types, 16 molecules B5BDBEBGBOBcBfBpB9ALAQAcAgAmAnAo

#6: Protein bL32m


Mass: 21537.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LTC4
#10: Protein Ribosomal_L2_C domain-containing protein


Mass: 33270.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287A143
#11: 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) / References: UniProt: A0A140UHW4
#13: Protein Ribosome-recycling factor, mitochondrial / RRF / Ribosome-releasing factor / mitochondrial


Mass: 28689.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRRF / Production host: Escherichia coli (E. coli) / References: UniProt: Q96E11
#18: Protein uL14m


Mass: 15955.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1V5Y7
#31: Protein TGS domain-containing protein


Mass: 38523.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UDR3
#34: Protein mL42


Mass: 16680.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BQA1
#45: Protein mL53


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


Mass: 10841.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1THS9
#65: Protein Mitoribosomal protein us12m, mrps12


Mass: 15257.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0M3KL52
#69: Protein uS17m


Mass: 14452.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RIU0
#75: Protein Interferon alpha-inducible protein 6 / 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) / References: UniProt: A0A0M3KL55
#79: Protein Death associated protein 3


Mass: 46966.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LS10
#84: Protein Coiled-coil-helix-coiled-coil-helix domain containing 1


Mass: 13561.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SU49
#85: Protein Aurora kinase A interacting protein 1


Mass: 22843.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B3R8
#86: Protein Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,mS39,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3


Mass: 76524.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SVC4

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RNA chain , 5 types, 5 molecules BBAAAVAXBA

#8: RNA chain CP tRNAPhe


Mass: 23402.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 45826169
#52: RNA chain 12S rRNA


Mass: 308989.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 11055671
#54: RNA chain tRNA (P/E)


Mass: 21713.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#55: RNA chain mRNA


Mass: 1485.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#56: RNA chain 16S rRNA


Mass: 504852.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 33320725

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28S ribosomal protein ... , 16 types, 16 molecules ABACAEAGAIAJANAOAPARAUAdAfAhAkAp

#57: Protein 28S ribosomal protein S2, mitochondrial / Mitochondrial ribosomal protein S2


Mass: 31731.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S001
#58: Protein 28S ribosomal protein S24, mitochondrial / Mitochondrial ribosomal protein S24


Mass: 18935.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ANU4
#59: 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) / References: UniProt: F1SU66
#61: Protein 28S ribosomal protein S7, mitochondrial / Mitochondrial ribosomal protein S7


Mass: 28150.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJ25
#62: Protein 28S ribosomal protein S9, mitochondrial / Mitochondrial ribosomal protein S9


Mass: 45604.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LU08
#63: Protein 28S ribosomal protein S10, mitochondrial


Mass: 23105.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RUU2
#66: Protein 28S ribosomal protein S14, mitochondrial / 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) / References: UniProt: A0A0M3KL53
#67: Protein 28S ribosomal protein S15, mitochondrial


Mass: 27411.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VVY1
#68: Protein 28S ribosomal protein S16, mitochondrial


Mass: 15182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JTD7
#70: Protein 28S ribosomal protein S18c, mitochondrial isoform 1 / Mitoribosomal protein bs18m / mrps18c


Mass: 16211.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0M3KL54
#71: Protein 28S ribosomal protein S21, mitochondrial / Mitochondrial ribosomal protein S21


Mass: 10682.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNB3
#76: Protein 28S ribosomal protein S26, mitochondrial / Mitochondrial ribosomal protein S26


Mass: 23637.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S8A5
#78: Protein 28S ribosomal protein S28, mitochondrial / Mitochondrial ribosomal protein S28 / Mitoribosomal protein ms28 / mrps28


Mass: 21014.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0M3KL56
#80: Protein 28S ribosomal protein S31, mitochondrial


Mass: 44091.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SQW0
#83: Protein 28S ribosomal protein S35, mitochondrial isoform 1


Mass: 37104.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SG95
#87: Protein 28S ribosomal protein S18b, mitochondrial / MRP-S18-b / Mrps18-b / 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) / References: UniProt: Q767K8

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Protein/peptide , 1 types, 1 molecules AZ

#72: Protein/peptide unknown


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unknown polypeptide modeled as poly-alanine / Source: (natural) Sus scrofa (pig)

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Non-polymers , 6 types, 341 molecules

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


Mass: 24.305 Da / Num. of mol.: 327 / Source method: obtained synthetically / Formula: Mg
#90: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#91: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#92: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#93: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#94: 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

Component
IDNameTypeEntity IDParent-IDSource
155S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E)RIBOSOME#1-#880MULTIPLE SOURCES
255S mammalian mitochondrial ribosomeRIBOSOME#1-#12, #14-#881NATURAL
3Ribosome-recycling factor, mitochondrialRIBOSOME#131RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa (pig)9823
23Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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 recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15545 / Symmetry type: POINT

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