5AJ3 | pdb_00005aj3

Structure of the small subunit of the mammalian mitoribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.3 of the entry. See complete history. 

Literature

Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome.

Greber, B.J., Bieri, P., Leibundgut, M., Leitner, A., Aebersold, R., Boehringer, D., Ban, N.

(2015) Science 348: 303-308

  • DOI: https://doi.org/10.1126/science.aaa3872
  • Primary Citation Related Structures: 
    5AJ3, 5AJ4

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 
    • Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 1,148.33 kDa 
  • Atom Count: 66,363 
  • Modeled Residue Count: 6,625 
  • Deposited Residue Count: 8,349 
  • Unique protein chains: 33
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US2M, MRPS2289Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US3M, MRPS24167Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1ST79 (Sus scrofa)
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US5M, MRPS5D [auth E]430Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SU66 (Sus scrofa)
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BS6M, MRPS6E [auth F]124Sus scrofaMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US7M, MRPS7F [auth G]242Sus scrofaMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US9M, MRPS9G [auth I]397Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL59 (Sus scrofa)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US10M, MRPS10H [auth J]201Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RUU2 (Sus scrofa)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US11M, MRPS11I [auth K]196Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US12M, MRPS12J [auth L]139Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL52 (Sus scrofa)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US14M, MRPS14K [auth N]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL53 (Sus scrofa)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US15M, MRPS15L [auth O]239Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BS16M, MRPS16M [auth P]135Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US17M, MRPS17N [auth Q]130Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1UDM1 (Sus scrofa)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BS18M, MRPS18CO [auth R]143Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL54 (Sus scrofa)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL19M, MRPL19P [auth T]14Sus scrofaMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BS21M, MRPS21Q [auth U]87Sus scrofaMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS22, MRPS22U [auth a]360Sus scrofaMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS23, MRPS23V [auth b]190Sus scrofaMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS25, MRPS25W [auth c]173Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL55 (Sus scrofa)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS26, MRPS26X [auth d]205Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S8A5 (Sus scrofa)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS27, MRPS27Y [auth e]336Sus scrofaMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS28, MRPS28Z [auth f]188Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL56 (Sus scrofa)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS29, MRPS29AA [auth g]397Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RLM4 (Sus scrofa)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS31, MRPS31BA [auth h]387Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RME2 (Sus scrofa)
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS33, MRPS33CA [auth i]106Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1V2H3 (Sus scrofa)
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS34, MRPS34DA [auth j]218Sus scrofaMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS35, MRPS35EA [auth k]325Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SG95 (Sus scrofa)
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS37, MRPS37FA [auth m]118Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1SZV4 (Sus scrofa)
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS38, MRPS38GA [auth n]199Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL57 (Sus scrofa)
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS39, MRPS39HA [auth o]692Sus scrofaMutation(s): 0 
UniProt
Find proteins for K7GKS8 (Sus scrofa)
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS40, MRPS18BIA [auth p]258Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q767K8 (Sus scrofa)
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
UNASSIGNED HELICESJA [auth s]16Sus scrofaMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
UNASSIGNED HELICESKA [auth z]17Sus scrofaMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
MITORIBOSOMAL 12S RRNA962Sus scrofa
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Entity ID: 18
MoleculeChains LengthOrganismImage
P-SITE AND A-SITE TRNAR [auth V],
T [auth Y]		64Sus scrofa
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Entity ID: 19
MoleculeChains LengthOrganismImage
MRNAS [auth X]13Sus scrofa
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP


Download:Ideal Coordinates CCD File
AG [auth g]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
CG [auth p],
YF [auth R],
ZF [auth c]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth g],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN1.9
RECONSTRUCTIONRELION1.2
RECONSTRUCTIONRELION1.3

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references, Other
  • Version 2.0: 2017-08-30
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2018-03-07
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 2.2: 2019-12-18
    Changes: Derived calculations, Other
  • Version 2.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary