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- PDB-5aj3: Structure of the small subunit of the mammalian mitoribosome -

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Basic information

Entry
Database: PDB / ID: 5aj3
TitleStructure of the small subunit of the mammalian mitoribosome
Components
  • (MITORIBOSOMAL PROTEIN ...) x 31
  • (UNASSIGNED HELICES) x 2
  • MITORIBOSOMAL 12S RRNA
  • MRNAMessenger RNA
  • P-SITE AND A-SITE TRNA
KeywordsRIBOSOME / TRANSLATION / MITOCHONDRIA / MAMMALIAN 55S MITORIBOSOME / MAMMALIAN 55S MITOCHONDRIAL RIBOSOME / 28S SMALL SUBUNIT / MRNA / TRNA / DECODING CENTER / CRYO-EM / SINGLE PARTICLE ANALYSIS
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial ribosome assembly / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosomal small subunit binding / organelle membrane / small ribosomal subunit rRNA binding / regulation of translation ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial ribosome assembly / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosomal small subunit binding / organelle membrane / small ribosomal subunit rRNA binding / regulation of translation / cell junction / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / apoptotic process / mitochondrion / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
Helix Hairpins - #1480 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S31 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial ...Helix Hairpins - #1480 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S31 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / 40S ribosomal protein rpS2 (S5p), N-terminal / 28S ribosomal protein S25, mitochondrial / Ribosomal protein S6/Translation elongation factor EF1B / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein S11/S14 / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / CHCH / CHCH domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Nucleic acid-binding proteins / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S5, C-terminal domain / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S17/S11 / Ribosomal protein S12/S23 / Ribosomal protein S9/S16 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S12/S23 / Ribosomal protein S17 / Ribosomal protein S9 signature. / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S12 signature. / Helix Hairpins / Nucleotidyltransferase; domain 5 / Thioredoxin-like superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / 28S ribosomal protein S14, mitochondrial / 28S ribosomal protein S18c, mitochondrial isoform 1 / Small ribosomal subunit protein mS25 / 28S ribosomal protein S28, mitochondrial ...GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / 28S ribosomal protein S14, mitochondrial / 28S ribosomal protein S18c, mitochondrial isoform 1 / Small ribosomal subunit protein mS25 / 28S ribosomal protein S28, mitochondrial / Mitoribosomal protein ms38, mrps38 / Mitoribosomal protein us9m, mrps9 / 28S ribosomal protein S17, mitochondrial / Death associated protein 3 / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein uS10m / : / 28S ribosomal protein S2, mitochondrial / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein mS33 / 28S ribosomal protein S35, mitochondrial isoform 1 / : / Mitochondrial ribosomal protein S24 / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein uS5m / : / : / Mitochondrial ribosomal protein S6 / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS40
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGreber, B.J. / Bieri, P. / Leibundgut, M. / Leitner, A. / Aebersold, R. / Boehringer, D. / Ban, N.
CitationJournal: Science / Year: 2015
Title: Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome.
Authors: Basil J Greber / Philipp Bieri / Marc Leibundgut / Alexander Leitner / Ruedi Aebersold / Daniel Boehringer / Nenad Ban /
Abstract: Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of ...Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of the porcine 55S mitoribosome at 3.8 angstrom resolution by cryo-electron microscopy and chemical cross-linking/mass spectrometry. The structure of the 28S subunit in the complex was resolved at 3.6 angstrom resolution by focused alignment, which allowed building of a detailed atomic structure including all of its 15 mitoribosomal-specific proteins. The structure reveals the intersubunit contacts in the 55S mitoribosome, the molecular architecture of the mitoribosomal messenger RNA (mRNA) binding channel and its interaction with transfer RNAs, and provides insight into the highly specialized mechanism of mRNA recruitment to the 28S subunit. Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity.
History
DepositionFeb 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references / Other
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / em_image_scans ...atom_site / em_image_scans / em_software / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _pdbx_validate_close_contact.auth_atom_id_1
Revision 2.1Mar 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity / entity_src_nat
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.src_method / _entity_src_nat.pdbx_organism_scientific
Revision 2.2Dec 18, 2019Group: Derived calculations / Other / Category: atom_sites / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
A: MITORIBOSOMAL 12S RRNA
B: MITORIBOSOMAL PROTEIN US2M, MRPS2
C: MITORIBOSOMAL PROTEIN US3M, MRPS24
E: MITORIBOSOMAL PROTEIN US5M, MRPS5
F: MITORIBOSOMAL PROTEIN BS6M, MRPS6
G: MITORIBOSOMAL PROTEIN US7M, MRPS7
I: MITORIBOSOMAL PROTEIN US9M, MRPS9
J: MITORIBOSOMAL PROTEIN US10M, MRPS10
K: MITORIBOSOMAL PROTEIN US11M, MRPS11
L: MITORIBOSOMAL PROTEIN US12M, MRPS12
N: MITORIBOSOMAL PROTEIN US14M, MRPS14
O: MITORIBOSOMAL PROTEIN US15M, MRPS15
P: MITORIBOSOMAL PROTEIN BS16M, MRPS16
Q: MITORIBOSOMAL PROTEIN US17M, MRPS17
R: MITORIBOSOMAL PROTEIN BS18M, MRPS18C
T: MITORIBOSOMAL PROTEIN BL19M, MRPL19
U: MITORIBOSOMAL PROTEIN BS21M, MRPS21
V: P-SITE AND A-SITE TRNA
X: MRNA
Y: P-SITE AND A-SITE TRNA
a: MITORIBOSOMAL PROTEIN MS22, MRPS22
b: MITORIBOSOMAL PROTEIN MS23, MRPS23
c: MITORIBOSOMAL PROTEIN MS25, MRPS25
d: MITORIBOSOMAL PROTEIN MS26, MRPS26
e: MITORIBOSOMAL PROTEIN MS27, MRPS27
f: MITORIBOSOMAL PROTEIN MS28, MRPS28
g: MITORIBOSOMAL PROTEIN MS29, MRPS29
h: MITORIBOSOMAL PROTEIN MS31, MRPS31
i: MITORIBOSOMAL PROTEIN MS33, MRPS33
j: MITORIBOSOMAL PROTEIN MS34, MRPS34
k: MITORIBOSOMAL PROTEIN MS35, MRPS35
m: MITORIBOSOMAL PROTEIN MS37, MRPS37
n: MITORIBOSOMAL PROTEIN MS38, MRPS38
o: MITORIBOSOMAL PROTEIN MS39, MRPS39
p: MITORIBOSOMAL PROTEIN MS40, MRPS18B
s: UNASSIGNED HELICES
z: UNASSIGNED HELICES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,148,327185
Polymers1,144,18837
Non-polymers4,139148
Water2,126118
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

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RNA chain , 3 types, 4 molecules AVYX

#1: RNA chain MITORIBOSOMAL 12S RRNA


Mass: 308989.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: GenBank: 223972359
#18: RNA chain P-SITE AND A-SITE TRNA


Mass: 17744.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: MIXTURE OF DIFFERENT MITOCHONDRIAL TRNA SPECIES, BUILT AS POLY-PYRIMIDINE AND POLY-PURINE
Source: (natural) Sus scrofa / Organ: LIVER
#19: RNA chain MRNA / Messenger RNA


Mass: 3545.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MIXTURE OF DIFFERENT MITOCHONDRIAL MRNA SPECIES, BUILT AS POLY-PYRIMIDINE
Source: (natural) Sus scrofa / Organ: LIVER

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MITORIBOSOMAL PROTEIN ... , 31 types, 31 molecules BCEFGIJKLNOPQRTUabcdefghijkmnop

#2: Protein MITORIBOSOMAL PROTEIN US2M, MRPS2


Mass: 31731.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1S001
#3: Protein MITORIBOSOMAL PROTEIN US3M, MRPS24


Mass: 19007.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1ST79
#4: Protein MITORIBOSOMAL PROTEIN US5M, MRPS5


Mass: 48213.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1SU66
#5: Protein MITORIBOSOMAL PROTEIN BS6M, MRPS6


Mass: 14283.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH BS18M / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: I3LEJ9*PLUS
#6: Protein MITORIBOSOMAL PROTEIN US7M, MRPS7


Mass: 28150.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1RVX4
#7: Protein MITORIBOSOMAL PROTEIN US9M, MRPS9


Mass: 45022.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: A0A0M3KL59*PLUS
#8: Protein MITORIBOSOMAL PROTEIN US10M, MRPS10


Mass: 23192.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1RUU2*PLUS
#9: Protein MITORIBOSOMAL PROTEIN US11M, MRPS11


Mass: 20841.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1SRT1
#10: Protein MITORIBOSOMAL PROTEIN US12M, MRPS12


Mass: 15257.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: A0A0M3KL52*PLUS
#11: Protein MITORIBOSOMAL PROTEIN US14M, MRPS14


Mass: 15120.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: A0A0M3KL53*PLUS
#12: Protein MITORIBOSOMAL PROTEIN US15M, MRPS15


Mass: 27411.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER
#13: Protein MITORIBOSOMAL PROTEIN BS16M, MRPS16


Mass: 15182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH MS25 / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1SU70
#14: Protein MITORIBOSOMAL PROTEIN US17M, MRPS17


Mass: 14452.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1RIU0
#15: Protein MITORIBOSOMAL PROTEIN BS18M, MRPS18C


Mass: 16211.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH BS6M / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: A0A0M3KL54*PLUS
#16: Protein/peptide MITORIBOSOMAL PROTEIN BL19M, MRPL19


Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER
#17: Protein MITORIBOSOMAL PROTEIN BS21M, MRPS21


Mass: 10682.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: I3L971
#20: Protein MITORIBOSOMAL PROTEIN MS22, MRPS22


Mass: 39599.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER
#21: Protein MITORIBOSOMAL PROTEIN MS23, MRPS23


Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER
#22: Protein MITORIBOSOMAL PROTEIN MS25, MRPS25


Mass: 19954.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH BS16M / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: A0A0M3KL55*PLUS
#23: Protein MITORIBOSOMAL PROTEIN MS26, MRPS26


Mass: 23637.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1S8A5
#24: Protein MITORIBOSOMAL PROTEIN MS27, MRPS27


Mass: 28613.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PPR FOLD / Source: (natural) Sus scrofa / Organ: LIVER
#25: Protein MITORIBOSOMAL PROTEIN MS28, MRPS28


Mass: 21014.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OB-FOLD / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: A0A0M3KL56*PLUS
#26: Protein MITORIBOSOMAL PROTEIN MS29, MRPS29


Mass: 44924.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: AAA ATPASE-LIKE FOLD / Source: (natural) Sus scrofa (pig) / Organ: LIVER / References: UniProt: F1RLM4*PLUS
#27: Protein MITORIBOSOMAL PROTEIN MS31, MRPS31


Mass: 44019.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1RME2
#28: Protein MITORIBOSOMAL PROTEIN MS33, MRPS33


Mass: 12544.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1S8G3
#29: Protein MITORIBOSOMAL PROTEIN MS34, MRPS34


Mass: 25681.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SH3-LIKE CORE FOLD / Source: (natural) Sus scrofa / Organ: LIVER
#30: Protein MITORIBOSOMAL PROTEIN MS35, MRPS35


Mass: 37104.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PEPTIDYL TRNA HYDROLASE FOLD / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1SG95
#31: Protein MITORIBOSOMAL PROTEIN MS37, MRPS37


Mass: 13561.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: F1SU49
#32: Protein MITORIBOSOMAL PROTEIN MS38, MRPS38


Mass: 22872.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: A0A0M3KL57*PLUS
#33: Protein MITORIBOSOMAL PROTEIN MS39, MRPS39


Mass: 62932.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PPR FOLD / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: K7GKS8
#34: Protein MITORIBOSOMAL PROTEIN MS40, MRPS18B


Mass: 29220.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER / References: UniProt: Q767K8

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Protein/peptide , 2 types, 2 molecules sz

#35: Protein/peptide UNASSIGNED HELICES


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER
#36: Protein/peptide UNASSIGNED HELICES


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa / Organ: LIVER

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Non-polymers , 4 types, 266 molecules

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


Mass: 24.305 Da / Num. of mol.: 144 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#39: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#40: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAIN F GB EW168165.2 CHAIN I GB NP_001231482.1 CHAIN J GB AK233895.1 CHAIN L GB AK394439.1 CHAIN N ...CHAIN F GB EW168165.2 CHAIN I GB NP_001231482.1 CHAIN J GB AK233895.1 CHAIN L GB AK394439.1 CHAIN N GB FD598185.1 CHAIN O GB AK343256.1 CHAIN R GB HX217955.1 CHAIN T UNP I3LNJ0 CHAIN a GB AK348087.1 CHAIN b GB XP_005669015.1 CHAIN c GB AK346624.1 CHAIN e GB XP_003134081.1 CHAIN f GB DN116920.1 CHAIN g GB XP_003361167.1 CHAIN j GB NP_001231761.1 CHAIN n GB AK231191.1 RESIDUES 251-266 OF uS9m (CHAIN I) BUILT AS UNK RESIDUES 309-356 OF mS22 (CHAIN a) BUILT AS UNK PPR FOLD OF mS27 (CHAIN e) BUILT AS UNK RESIDUES 52-69 OF mS29 (CHAIN g) BUILT AS UNK RESIDUES 152-158 OF mS34 (CHAIN j) BUILT AS UNK N-TERMINAL SEQUENCE OF mS38 (CHAIN n) IS MISSING PPR FOLD OF mS39 (CHAIN o) BUILT AS UNK ALL RESIDUES OF CHAINS s,z (UNASSIGNED HELICES AND FOLDS) BUILT AS UNK N-TERMINAL RESIDUES 54-67 OF bL19m (CHAIN T) BUILT AS UNK mRNA (CHAIN X) BUILT AS POLY-PYRIMIDINE A- AND P-SITE tRNAs (CHAINS Y,V) BUILT AS POLY-PYRIMIDINE AND POLY-PURINE

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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

ComponentName: SUS SCROFA 55S MITOCHONDRIAL RIBOSOME / Type: RIBOSOME
Details: QUANTIFOIL HOLEY CARBON GRIDS WERE COATED WITH A THIN CARBON FILM
Buffer solutionName: 20 MM HEPES-KOH, 50 MM KCL, 40 MM MGCL2, 1 MM DTT / pH: 7.4 / Details: 20 MM HEPES-KOH, 50 MM KCL, 40 MM MGCL2, 1 MM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE / Details: MIXTURE OF LIQUID ETHANE AND PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 30, 2014
Details: IMAGES WERE ACQUIRED IN 2 SESSIONS ON A FEI TITAN KRIOS IN MAY 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 100000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderTemperature: 85 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2UCSF Chimeramodel fitting
3EMAN1.93D reconstruction
4RELION1.23D reconstruction
5RELION1.33D reconstruction
CTF correctionDetails: PER DETECTOR FRAME
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MAXIMUM LIKELIHOOD BASED REFINEMENT IMPLEMENTED IN RELION
Resolution: 3.6 Å / Num. of particles: 78783 / Actual pixel size: 1.39 Å
Details: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--HIGH RESOLUTION CRYO-EM
RefinementHighest resolution: 3.6 Å
Refinement stepCycle: LAST / Highest resolution: 3.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43112 22958 175 118 66363

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