[English] 日本語
Yorodumi
- PDB-8oiq: 39S mammalian mitochondrial large ribosomal subunit with mtRF1 an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oiq
Title39S mammalian mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA
Components
  • (39S ribosomal protein ...) x 11
  • (Mitochondrial ribosomal protein ...) x 27
  • 16S rRNA
  • CP Phe-tRNA
  • E-site tRNA
  • ICT1
  • P-site Met-tRNA(fMet)
  • Peptide chain release factor 1, mitochondrial
  • Ribosomal protein
  • bL17m
  • bL31m
  • bL33m
  • mL42
  • mL44
  • mL54
  • mL62 (ICT1)
  • mL64Microsoft Macro Assembler
  • uL16m
  • uL22m
  • uL24m
  • uL30m
KeywordsRIBOSOME / mammalian mitochondrial ribosome / release factor mtRF1 / non-canonical stop codon
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / translation release factor activity, codon specific / ribonuclease III activity ...Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / translation release factor activity, codon specific / ribonuclease III activity / ribosomal subunit / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / organelle membrane / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / double-stranded RNA binding / large ribosomal subunit / cell junction / negative regulation of translation / rRNA binding / nuclear body / ribosome / structural constituent of ribosome / ribonucleoprotein complex / cell cycle / translation / protein domain specific binding / nucleotide binding / intracellular membrane-bounded organelle / mRNA binding / synapse / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, mitochondrial / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Ribosomal protein L37, mitochondrial / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial ...Ribosomal protein L1, mitochondrial / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / 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 / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein L37/S30 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / MRPL44, double-stranded RNA binding domain / Tim44-like domain / Tim44-like domain / Tim44 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / 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 / 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 / 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. / TGS / TGS-like / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / : / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Beta-grasp domain superfamily / NTF2-like domain superfamily / Ribosomal protein L1, 3-layer alpha/beta-sandwich / NUDIX hydrolase-like domain superfamily / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L35
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / N-FORMYLMETHIONINE / : / PHENYLALANINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...FE2/S2 (INORGANIC) CLUSTER / N-FORMYLMETHIONINE / : / PHENYLALANINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL28m / 39S ribosomal protein L20, mitochondrial isoform 1 / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein mL64 / 39S ribosomal protein L49, mitochondrial / Large ribosomal subunit protein bL34m / Mitochondrial ribosomal protein L2 / Ribosomal protein / Large ribosomal subunit protein uL1m / Mitochondrial ribosomal protein L12 / 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 / 39S ribosomal protein L48, mitochondrial / Large ribosomal subunit protein uL23m / 39S ribosomal protein S30, mitochondrial / Mitochondrial ribosomal protein L18 / 39S ribosomal protein L35, mitochondrial / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL22m / Mitochondrial ribosomal protein S18A / 39S ribosomal protein L27, mitochondrial / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein uL29m / Mitochondrial ribosomal protein L39 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein uL30m / 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 / 39S ribosomal protein L13, mitochondrial / Peptide chain release factor 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSaurer, M. / Leibundgut, M. / Scaiola, A. / Schoenhut, T. / Ban, N.
Funding support Switzerland, European Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation179190 Switzerland
Swiss National Science Foundation182341 Switzerland
European Molecular Biology Organization (EMBO)1074-2019European Union
CitationJournal: Science / Year: 2023
Title: Molecular basis of translation termination at noncanonical stop codons in human mitochondria.
Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / ...Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / David Gatfield / Aleksandra Filipovska / Nenad Ban /
Abstract: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the ...The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _em_3d_fitting_list.initial_refinement_model_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B1: Mitochondrial ribosomal protein L12
B2: Mitochondrial ribosomal protein L12
B3: Mitochondrial ribosomal protein L12
B4: Mitochondrial ribosomal protein L12
B5: Mitochondrial ribosomal protein L12
B6: Mitochondrial ribosomal protein L12
B7: E-site tRNA
B8: 16S rRNA
B9: CP Phe-tRNA
BA: uL22m
BB: 39S ribosomal protein L23, mitochondrial
BC: uL24m
BD: Mitochondrial ribosomal protein L27
BE: Mitochondrial ribosomal protein L28
BF: Mitochondrial ribosomal protein L47
BG: uL30m
BH: Mitochondrial ribosomal protein L32
BI: bL33m
BJ: Mitochondrial ribosomal protein L34
BK: 39S ribosomal protein L35, mitochondrial
BL: Mitochondrial ribosomal protein L2
BM: ICT1
BN: Mitochondrial ribosomal protein L4
BO: Mitochondrial ribosomal protein L9
BP: Mitochondrial ribosomal protein L10
BQ: Mitochondrial ribosomal protein L11
BR: 39S ribosomal protein L13, mitochondrial
BS: Mitochondrial ribosomal protein L14
BT: 39S ribosomal protein L15, mitochondrial
BU: uL16m
BV: bL17m
BW: Mitochondrial ribosomal protein L18
BX: 39S ribosomal protein L19, mitochondrial
BY: Mitochondrial ribosomal protein L20
BZ: Mitochondrial ribosomal protein L21
Ba: 39S ribosomal protein L52, mitochondrial
Bb: Mitochondrial ribosomal protein L53
Bc: mL54
Bd: bL31m
Be: Mitochondrial ribosomal protein L57
Bf: mL62 (ICT1)
Bg: mL64
Bh: Mitochondrial ribosomal protein S18A
Bi: 39S ribosomal protein S30, mitochondrial
Bj: 39S ribosomal protein L1, mitochondrial
Bl: Ribosomal protein
Bm: Mitochondrial ribosomal protein L37
Bn: Mitochondrial ribosomal protein L38
Bo: Mitochondrial ribosomal protein L39
Bp: Mitochondrial ribosomal protein L40
Bq: Mitochondrial ribosomal protein L41
Br: mL42
Bs: 39S ribosomal protein L43, mitochondrial isoform X2
Bt: mL44
Bu: Mitochondrial ribosomal protein L45
Bv: Mitochondrial ribosomal protein L46
Bw: 39S ribosomal protein L48, mitochondrial
Bx: 39S ribosomal protein L49, mitochondrial
By: Mitochondrial ribosomal protein L50
Bz: Mitochondrial ribosomal protein L51
AG: P-site Met-tRNA(fMet)
Aa: Peptide chain release factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,024,945302
Polymers2,018,14162
Non-polymers6,805240
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area409240 Å2
ΔGint-4253 kcal/mol
Surface area590780 Å2

-
Components

+
Mitochondrial ribosomal protein ... , 27 types, 32 molecules B1B2B3B4B5B6BDBEBFBHBJBLBNBOBPBQBSBWBYBZBbBeBhBmBnBoBpBqBuBvByBz

#1: Protein
Mitochondrial ribosomal protein L12


Mass: 21268.975 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287ARV8
#8: Protein Mitochondrial ribosomal protein L27


Mass: 15943.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RT79
#9: Protein Mitochondrial ribosomal protein L28 /


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


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


Mass: 23567.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3LTC4
#14: Protein Mitochondrial ribosomal protein L34


Mass: 10871.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287A119
#16: Protein Mitochondrial ribosomal protein L2


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


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


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


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


Mass: 20809.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_003122536.1 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RU54
#23: Protein Mitochondrial ribosomal protein L14


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


Mass: 21422.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_003121157.1 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A4X1VX01
#29: Protein Mitochondrial ribosomal protein L20


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


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


Mass: 12057.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_020942999.1 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A8D0LKT0
#35: Protein Mitochondrial ribosomal protein L57


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


Mass: 22273.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_005654252.2 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RRH6
#42: Protein Mitochondrial ribosomal protein L37 /


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


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


Mass: 38523.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_003132793.4 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SHP6
#45: Protein Mitochondrial ribosomal protein L40


Mass: 19406.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZP98
#46: 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) / Organ: Liver / References: UniProt: A0A287AWS0
#50: Protein Mitochondrial ribosomal protein L45


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


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


Mass: 22785.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3L9H6
#55: Protein Mitochondrial ribosomal protein L51


Mass: 15249.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287BE26

-
RNA chain , 4 types, 4 molecules B7B8B9AG

#2: RNA chain E-site tRNA


Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: likely the CCA-end of a tRNA / Source: (natural) Sus scrofa (pig) / Organ: Liver
#3: RNA chain 16S rRNA /


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


Mass: 23516.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver
#56: RNA chain P-site Met-tRNA(fMet)


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

-
Protein , 15 types, 15 molecules BABCBGBIBMBUBVBcBdBfBgBlBrBtAa

#5: Protein uL22m


Mass: 24313.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1RQC9
#7: Protein uL24m


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


Mass: 18921.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1STE5
#13: Protein bL33m


Mass: 7508.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A286ZU68
#17: Protein ICT1 / Mitochondrial ribosomal protein L3


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


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


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


Mass: 15957.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_003123104.1 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3LN63
#34: Protein bL31m


Mass: 15156.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: I3L9J0
#36: Protein mL62 (ICT1)


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


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


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


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


Mass: 37527.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1SR64
#57: Protein Peptide chain release factor 1, mitochondrial / MRF-1 / MtRF-1


Mass: 55569.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human mitochondrial release factor 1 (mtRF1), with a C-terminal linker (GGSGGSG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) plasmid in HEK293 EBNA cells.
Source: (gene. exp.) Homo sapiens (human) / Gene: MTRF1 / Plasmid: pcDNA3.1(+) / Cell line (production host): HEK293 EBNA / Production host: Homo sapiens (human) / References: UniProt: O75570

-
39S ribosomal protein ... , 11 types, 11 molecules BBBKBRBTBXBaBiBjBsBwBx

#6: Protein 39S ribosomal protein L23, mitochondrial / Ribosome


Mass: 17685.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A480JJI1
#15: Protein 39S ribosomal protein L35, mitochondrial / Ribosome


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


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


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


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


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


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


Mass: 34372.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287AF82
#48: Protein 39S ribosomal protein L43, mitochondrial isoform X2 / Ribosome


Mass: 17770.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: F1S8U4
#52: Protein 39S ribosomal protein L48, mitochondrial / Ribosome / 39S ribosomal protein L48 / mitochondrial isoform 1 / Mitochondrial ribosomal protein L48


Mass: 29942.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A480J9Z6
#53: Protein 39S ribosomal protein L49, mitochondrial / Ribosome


Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: NP_001231942.1 / Source: (natural) Sus scrofa (pig) / Organ: Liver / References: UniProt: A0A287A0K2

-
Non-polymers , 6 types, 240 molecules

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


Mass: 24.305 Da / Num. of mol.: 205 / Source method: obtained synthetically / Formula: Mg
#59: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: K
#60: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#62: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#63: Chemical ChemComp-FME / N-FORMYLMETHIONINE / N-Formylmethionine


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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 39S mammalian mitochondrial ribosome with mtRF1 and P-site tRNAMet
Type: RIBOSOME
Details: Mammalian mitochondrial translation termination complex, in vitro reconstituted from porcine mitoribosomal subunits, human mtRF1-3xFLAG, human methionine-tRNA(formyl-methionine), and a ...Details: Mammalian mitochondrial translation termination complex, in vitro reconstituted from porcine mitoribosomal subunits, human mtRF1-3xFLAG, human methionine-tRNA(formyl-methionine), and a synthetic mRNA (5'-A AUG AGA CAA-3') containing the non-canonical stop codon AGA. Refined with focus on the large subunit.
Entity ID: #1-#57 / Source: NATURAL
Molecular weightValue: 1.5 MDa / Experimental value: NO
Source (natural)Organism: Sus scrofa (pig) / Cellular location: Mitochondrial matrix / Organ: Liver / Organelle: Mitochondria
Buffer solutionpH: 7.5
Details: 20mM HEPES-KOH pH=7.5, 100mM KCl, 20mM MgCl2, ~1% sucrose (from mtRF1 storage buffer)
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMpotassium chlorideKCl1
320 mMmagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: In vitro reconstituted complex (55S). Focused refinement on large subunit.
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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 FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6973
EM imaging opticsEnergyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
4cryoSPARC4CTF correction
7Coot0.9.8.4model fitting
9cryoSPARC4initial Euler assignment
11cryoSPARC4classification
12cryoSPARC3D reconstruction
13PHENIX1.20.1model refinement
Image processingDetails: Micrographs were motion corrected and CTF parameters were estimated using Cryosparc live v4.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1471587
Details: Particles were picked with blob picker in Cryosparc live v4.
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50622 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeDetailsInitial refinement model-IDSource nameType
17NQH

7nqh

7NQHSus scrofa mitoribosome1PDBexperimental model
27QI4

7qi4

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

+
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