[English] 日本語
Yorodumi
- PDB-7nqh: 55S mammalian mitochondrial ribosome with mtRF1a and P-site tRNAMet -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nqh
Title55S mammalian mitochondrial ribosome with mtRF1a and P-site tRNAMet
Components
  • (28S ribosomal protein ...) x 3
  • (39S ribosomal protein ...) x 2
  • (Mitochondrial ribosomal protein ...) x 38
  • 12S rRNA
  • 16S rRNA
  • Aurora kinase A interacting protein 1
  • Death associated protein 3
  • ICT1
  • Mitoribosomal protein ms28, mrps28
  • Mrpl34
  • Pentatricopeptide repeat domain 3
  • Peptide chain release factor 1-like, mitochondrial
  • Ribosomal protein
  • bL17m
  • bL31m
  • bL32m
  • bL33m
  • bS21m
  • bS6m
  • mL40
  • mL42
  • mL44
  • mL52
  • mL53
  • mL54
  • mL62 (ICT1)
  • mL64
  • mRNA
  • mS23
  • mS33
  • mS34
  • mS37
  • tRNA(Phe) in LSU
  • tRNAMet
  • uL13m
  • uL14m
  • uL15m
  • uL16m
  • uL22m
  • uL23m
  • uL24m
  • uL2m
  • uL30m
  • uS11m
  • uS15m
  • uS17m
  • uS9m
  • unknown
KeywordsTRANSLATION / Ribosome / Mitochondria / Termination / mtRF1a / Release
Function / homology
Function and homology information


Hormone ligand-binding receptors / G alpha (q) signalling events / gonadotropin hormone-releasing hormone activity / gonadotropin-releasing hormone receptor binding / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / translation release factor activity, codon specific ...Hormone ligand-binding receptors / G alpha (q) signalling events / gonadotropin hormone-releasing hormone activity / gonadotropin-releasing hormone receptor binding / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / translation release factor activity, codon specific / mitochondrial translational elongation / ribonuclease III activity / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / translation release factor activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / mitochondrial translation / organelle membrane / apoptotic mitochondrial changes / positive regulation of proteolysis / ribosomal small subunit binding / RNA processing / rescue of stalled ribosome / cell junction / large ribosomal subunit / double-stranded RNA binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / negative regulation of translation / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / intracellular membrane-bounded organelle / mRNA binding / positive regulation of DNA-templated transcription / nucleolus / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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 / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / : / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal protein S23 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / Mitochondrial 28S ribosomal protein S34 / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / : / Mitochondrial ribosome subunit S24 / Small ribosomal subunit protein uS5m, N-terminal / Small ribosomal subunit protein mS39, PPR / 28S ribosomal protein S25, mitochondrial / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial 28S ribosomal protein S32 / Mitochondrial ribosomal subunit protein / 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) / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : / MRPL44, double-stranded RNA binding domain / : / MRPL44 dsRNA-binding domain / Large ribosomal subunit protein mL44, endonuclease domain / : / : / Large ribosomal subunit protein bL9m C-terminal domain / Large ribosomal subunit protein bL9m N-terminal domain / Tim44-like domain / Tim44-like domain / Pentatricopeptide (PPR) repeat profile. / Tim44 / : / : / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein S23/S29, mitochondrial / Ribosomal protein L7/L12 C-terminal domain / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SPERMINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SPERMINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12m / 28S ribosomal protein S14, mitochondrial / Small ribosomal subunit protein bS18m / 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 / Small ribosomal subunit protein uS11m / Large ribosomal subunit protein mL62 / 28S ribosomal protein S21, mitochondrial / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein bL20m / 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 S23 / 28S ribosomal protein S24, mitochondrial / Mitochondrial ribosomal protein S22 / Large ribosomal subunit protein bL12m / Mitochondrial ribosomal protein S34 / Mitochondrial ribosomal protein L41 / Progonadoliberin / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein mL37 / Small ribosomal subunit protein uS15m / Large ribosomal subunit protein uL14m / Mitochondrial ribosomal protein L57 / Large ribosomal subunit protein mL42 / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein mL48 / Small ribosomal subunit protein bS16m / 39S ribosomal protein S30, mitochondrial / Small ribosomal subunit protein mS27 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein mS31 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein mL66 / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / Large ribosomal subunit protein bL27m / 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 / Small ribosomal subunit protein uS2m / 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 mL39 / 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 / 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 mL54 / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL9m / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein bL32m / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein mS39 / Large ribosomal subunit protein uL13m / Small ribosomal subunit protein mS40 / Peptide chain release factor 1-like, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12527
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
BB: tRNA(Phe) in LSU
BD: uL2m
BE: ICT1
BF: Mitochondrial ribosomal protein L4
BI: Mitochondrial ribosomal protein L9
BJ: Mitochondrial ribosomal protein L10
BK: Mitochondrial ribosomal protein L11
BL: Peptide chain release factor 1-like, mitochondrial
BN: uL13m
BO: uL14m
BP: uL15m
BQ: uL16m
BR: bL17m
BS: Mitochondrial ribosomal protein L18
BT: Mitochondrial ribosomal protein L19
BU: Mitochondrial ribosomal protein L20
BV: Mitochondrial ribosomal protein L21
BW: uL22m
BX: uL23m
BY: uL24m
Ba: Mitochondrial ribosomal protein L37
Bb: Mitochondrial ribosomal protein L38
B3: uL30m
Bc: Mitochondrial ribosomal protein L39
Bd: mL40
Be: Mitochondrial ribosomal protein L41
Bf: mL42
Bg: Mitochondrial ribosomal protein L43
Bh: mL44
Bi: Mitochondrial ribosomal protein L45
Bj: Mitochondrial ribosomal protein L46
Bk: 39S ribosomal protein L48, mitochondrial
Bl: Mrpl34
Bm: Mitochondrial ribosomal protein L50
Bn: Mitochondrial ribosomal protein L51
Bo: mL52
Bp: mL53
Bq: mL54
Bt: Mitochondrial ribosomal protein L57
Bu: mL62 (ICT1)
Bv: mL64
Bw: 39S ribosomal protein S30, mitochondrial
Bx: Mitochondrial ribosomal protein S18A
AA: 12S rRNA
B4: bL31m
B5: bL32m
B6: bL33m
B7: Mitochondrial ribosomal protein L34
AB: Mitochondrial ribosomal protein S2
AC: Mitochondrial ribosomal protein S24
AE: Mitochondrial ribosomal protein S5
AF: bS6m
AG: 28S ribosomal protein S7, mitochondrial
AI: uS9m
AJ: Mitochondrial ribosomal protein S10
AK: uS11m
AL: Mitochondrial ribosomal protein S12
AN: Mitochondrial ribosomal protein S14
AO: uS15m
AP: 28S ribosomal protein S16, mitochondrial
AQ: uS17m
AR: Mitochondrial ribosomal protein S18C
AU: bS21m
AV: tRNAMet
AX: mRNA
AZ: unknown
Aa: Mitochondrial ribosomal protein S22
Ab: mS23
Ac: Mitochondrial ribosomal protein S25
Ad: Mitochondrial ribosomal protein S26
B8: Mitochondrial ribosomal protein L35
Ae: Mitochondrial ribosomal protein S27
Af: Mitoribosomal protein ms28, mrps28
Ag: Death associated protein 3
Ah: Mitochondrial ribosomal protein S31
Ai: mS33
Aj: mS34
Ak: Mitochondrial ribosomal protein S35
Am: mS37
An: Aurora kinase A interacting protein 1
Ao: Pentatricopeptide repeat domain 3
Ap: 28S ribosomal protein S18b, mitochondrial
B9: Ribosomal protein
BA: 16S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,121,263428
Polymers3,111,16493
Non-polymers10,100335
Water543
1


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

-
Components

+
Mitochondrial ribosomal protein ... , 38 types, 43 molecules CLDLELFLGLHLB0B1B2BFBIBJBKBSBTBUBVBaBbBcBeBgBiBjBmBnBtBxB7AB...

#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) / 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) / 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) / 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) / References: UniProt: F1SGC7
#8: 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
#9: 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) / References: UniProt: I3LR45
#10: 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
#11: Protein Mitochondrial ribosomal protein L11


Mass: 20809.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 178-192 built as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RU54
#18: 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
#19: Protein Mitochondrial ribosomal protein L19


Mass: 33441.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 62 - 70 modeled as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LNJ0
#20: 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) / References: UniProt: A0A286ZU56
#21: 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) / References: UniProt: F1RY70
#25: 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
#26: 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) / References: UniProt: F1RW03
#28: 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
#30: 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
#32: 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
#34: 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
#35: 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
#38: 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) / References: UniProt: I3L9H6
#39: 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) / References: UniProt: A0A287BE26
#43: 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
#47: 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
#52: 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) / References: UniProt: A0A287A119
#53: 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) / References: UniProt: F1S001
#54: 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) / References: UniProt: A0A287ANU4
#55: Protein 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
#59: 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) / References: UniProt: F1RUU2
#61: 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) / References: UniProt: A0A0M3KL52
#62: 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) / References: UniProt: A0A0M3KL53
#66: 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) / References: UniProt: A0A0M3KL54
#71: 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
#73: 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) / References: UniProt: A0A0M3KL55
#74: 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) / References: UniProt: A0A287AY01
#75: 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
#76: Protein Mitochondrial ribosomal protein S27


Mass: 51945.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 337-352 built as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2R5D6
#79: Protein Mitochondrial ribosomal protein S31


Mass: 44091.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RME2
#82: Protein Mitochondrial ribosomal protein S35


Mass: 37104.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SG95

-
RNA chain , 5 types, 5 molecules BBAAAVAXBA

#5: RNA chain tRNA(Phe) in LSU


Mass: 23402.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 76262549
#48: 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
#68: RNA chain tRNAMet


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


Mass: 2839.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#88: 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

+
Protein , 39 types, 39 molecules BDBEBLBNBOBPBQBRBWBXBYB3BdBfBhBlBoBpBqBuBvB4B5B6AFAIAKAOAQAU...

#6: Protein uL2m


Mass: 33270.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRN2
#7: 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
#12: Protein Peptide chain release factor 1-like, mitochondrial / Mitochondrial translational release factor 1-like / mtRF1a


Mass: 41166.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mtRF1a (residues 33-380) with N-terminal GS-linker / Source: (gene. exp.) Homo sapiens (human) / Gene: MTRF1L, MTRF1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGC7
#13: Protein uL13m


Mass: 20633.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GP19
#14: Protein uL14m


Mass: 15955.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BMZ6
#15: Protein uL15m


Mass: 33481.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RSH0
#16: Protein uL16m


Mass: 28680.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RI89
#17: Protein bL17m


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 uL22m


Mass: 24313.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RQC9
#23: Protein uL23m


Mass: 17643.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 115-133 built as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZZC6
#24: Protein uL24m


Mass: 24893.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RHJ1
#27: Protein uL30m


Mass: 18921.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1STE5
#29: Protein mL40


Mass: 24075.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZP98
#31: Protein mL42


Mass: 16680.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 77-100 built as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BQA1
#33: Protein mL44


Mass: 37527.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SR64
#37: 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
#40: Protein mL52


Mass: 13813.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S9B7
#41: Protein mL53


Mass: 12015.747 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A341D604
#42: Protein mL54


Mass: 15957.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Residues 71-87 built as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LN63
#44: Protein mL62 (ICT1)


Mass: 23545.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 86-92 built as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJR2
#45: Protein mL64


Mass: 25815.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZXA6
#49: Protein bL31m


Mass: 15156.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 83-96 built as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L9J0
#50: 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
#51: Protein bL33m


Mass: 7508.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZU68
#56: Protein bS6m


Mass: 30365.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LEJ9
#58: Protein uS9m


Mass: 45604.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LU08
#60: Protein uS11m


Mass: 20841.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJJ6
#63: Protein uS15m


Mass: 27411.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BMP0
#65: 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
#67: Protein bS21m


Mass: 10682.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNB3
#72: Protein mS23


Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AEW3
#77: 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) / References: UniProt: A0A0M3KL56
#78: 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
#80: Protein mS33


Mass: 12544.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S8G3
#81: Protein mS34


Mass: 25843.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AVS9
#83: Protein mS37


Mass: 13561.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SU49
#84: 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
#85: Protein Pentatricopeptide repeat domain 3


Mass: 79343.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 201-234 built as poly-Alanine / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GKS8
#87: 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: A0A287A731

-
39S ribosomal protein ... , 2 types, 2 molecules BkBw

#36: 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
#46: 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

-
28S ribosomal protein ... , 3 types, 3 molecules AGAPAp

#57: Protein 28S ribosomal protein S7, mitochondrial / Mitochondrial ribosomal protein S7


Mass: 27778.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJ25
#64: 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) / References: UniProt: A0A480JTD7
#86: 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) / References: UniProt: Q767K8

-
Protein/peptide , 1 types, 1 molecules AZ

#70: 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)

-
Non-polymers , 6 types, 338 molecules

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


Mass: 24.305 Da / Num. of mol.: 323 / 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#93: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#94: Water ChemComp-HOH / water


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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1translation termination complex of mitochondrial ribosome with release factor mtRF1a and P-site tRNAMetRIBOSOME#1-#880MULTIPLE SOURCES
2translation termination complex of mitochondrial ribosomeRIBOSOME#1-#11, #13-#67, #70-#881NATURAL
3Peptide chain release factor 1-like, mitochondrialRIBOSOME#121RECOMBINANT
4RNARIBOSOME#68-#691RECOMBINANT
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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
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)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47048 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more