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- PDB-7nsh: 39S mammalian mitochondrial large ribosomal subunit with mtRRF (p... -

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Basic information

Entry
Database: PDB / ID: 7nsh
Title39S mammalian mitochondrial large ribosomal subunit with mtRRF (post) and mtEFG2
Components
  • (39S ribosomal protein ...) x 2
  • (Mitochondrial ribosomal protein ...) x 26
  • 16S rRNA
  • CP tRNAPhe
  • ICT1
  • Mrpl34
  • Ribosomal protein
  • Ribosome-recycling factor, mitochondrial
  • Ribosome-releasing factor 2, mitochondrial
  • bL17m
  • bL31m
  • bL32m
  • bL33m
  • mL42
  • mL44
  • mL52
  • mL53
  • mL54
  • mL62 (ICT1)
  • mL64
  • uL13m
  • uL14m
  • uL15m
  • uL16m
  • uL22m
  • uL23m
  • uL24m
  • uL2m
  • uL30m
KeywordsTRANSLATION / Ribosome / Mitochondria
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / ribonuclease III activity / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / mitochondrial large ribosomal subunit ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / ribonuclease III activity / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / ribosome disassembly / peptidyl-tRNA hydrolase activity / mitochondrial translation / organelle membrane / ribosomal large subunit binding / RNA processing / rescue of stalled ribosome / cell junction / double-stranded RNA binding / large ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial inner 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 / GTPase activity / mRNA binding / positive regulation of DNA-templated transcription / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ribosome-releasing factor 2, mitochondrial / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / : / Elongation factor G domain 2 / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily ...Ribosome-releasing factor 2, mitochondrial / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / : / Elongation factor G domain 2 / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Elongation factor G, domain III / EFG, domain V / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L37, mitochondrial / 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 / 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 L7/L12 C-terminal domain / 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 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / 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-like / TGS domain profile. / TGS / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Elongation Factor G, domain II / Elongation Factor G, domain III / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / :
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein mL49 ...GUANOSINE-5'-MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein uL18m / 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 / Large ribosomal subunit protein bL12m / Mitochondrial ribosomal protein L41 / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein uL14m / Mitochondrial ribosomal protein L57 / Large ribosomal subunit protein mL42 / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein mL48 / 39S ribosomal protein S30, mitochondrial / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / 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 / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL52 / 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 / 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 bL19m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein uL13m / Ribosome-releasing factor 2, mitochondrial / Ribosome-recycling factor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 1.0May 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 1.2Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
B0: Mitochondrial ribosomal protein L27
BY: uL24m
Ba: Mitochondrial ribosomal protein L37
B8: Mitochondrial ribosomal protein L35
Bb: Mitochondrial ribosomal protein L38
Bc: Mitochondrial ribosomal protein L39
Bd: Mitochondrial ribosomal protein L40
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
CL: Mitochondrial ribosomal protein L12
B1: Mitochondrial ribosomal protein L28
DL: Mitochondrial ribosomal protein L12
EL: Mitochondrial ribosomal protein L12
FL: Mitochondrial ribosomal protein L12
B9: Ribosomal protein
GL: Mitochondrial ribosomal protein L12
HL: Mitochondrial ribosomal protein L12
BA: 16S rRNA
B2: Mitochondrial ribosomal protein L47
B3: uL30m
B4: bL31m
B5: bL32m
B6: bL33m
B7: Mitochondrial ribosomal protein L34
BB: CP tRNAPhe
BC: Ribosome-releasing factor 2, mitochondrial
BD: uL2m
BG: Ribosome-recycling factor, mitochondrial
BQ: uL16m
LL: Mitochondrial ribosomal protein L12
BE: ICT1
BF: Mitochondrial ribosomal protein L4
BI: Mitochondrial ribosomal protein L9
BJ: Mitochondrial ribosomal protein L10
BK: Mitochondrial ribosomal protein L11
BN: uL13m
BO: uL14m
BP: uL15m
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,021,114290
Polymers2,013,89361
Non-polymers7,221229
Water362
1


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

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Components

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Mitochondrial ribosomal protein ... , 26 types, 32 molecules B0BaB8BbBcBdBeBgBiBjBmBnBtBxCLDLELFLGLHLLLB1B2B7BFBIBJBKBSBTBUBV

#1: 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 L37


Mass: 47917.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BIV6
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#10: 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
#12: 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
#13: 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
#16: 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
#17: 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
#21: 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
#25: 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
#26: Protein
Mitochondrial ribosomal protein L12


Mass: 21268.975 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ARV8
#27: 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
#30: 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
#35: 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
#42: 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
#43: 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
#44: 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
#45: Protein Mitochondrial ribosomal protein L11


Mass: 20809.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RU54
#50: 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
#51: 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) / References: UniProt: I3LNJ0
#52: 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
#53: 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

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Protein , 25 types, 25 molecules BYBfBhBlBoBpBqBuBvB9B3B4B5B6BCBDBGBQBEBNBOBPBRBWBX

#2: 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
#9: 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
#11: 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
#15: 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
#18: 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
#19: 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
#20: Protein mL54


Mass: 15957.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LN63
#22: Protein mL62 (ICT1)


Mass: 23545.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJR2
#23: 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
#28: 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
#31: 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
#32: Protein bL31m


Mass: 15156.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L9J0
#33: 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
#34: 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
#37: Protein Ribosome-releasing factor 2, mitochondrial / RRF2mt / Elongation factor G 2 / mitochondrial / EF-G2mt / mEF-G 2 / Elongation factor G2 / hEFG2


Mass: 83848.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFM2, EFG2, MSTP027 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969S9
#38: 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
#39: 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
#40: 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
#41: 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
#46: 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
#47: 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
#48: 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
#49: 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
#54: 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
#55: Protein uL23m


Mass: 17643.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZZC6

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

#14: 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
#24: 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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RNA chain , 2 types, 2 molecules BABB

#29: 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
#36: 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: 76262549

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Non-polymers , 6 types, 231 molecules

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


Mass: 24.305 Da / Num. of mol.: 221 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#60: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#61: 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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Details

Has ligand of interestY

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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
139S mammalian mitochondrial large ribosomal subunit with mtRRF (post) and mtEFG2RIBOSOME#1-#550MULTIPLE SOURCES
3mtRRF (post) and mtEFG2RIBOSOME#37, #391RECOMBINANT
239S mammalian mitochondrial large ribosomal subunitRIBOSOME#1-#36, #38, #40-#551NATURAL
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224731 / Symmetry type: POINT

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