5AJ3

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 

wwPDB Validation   3D Report Full Report


This is version 2.2 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: 10.1126/science.aaa3872
  • Primary Citation of 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 ...

    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. ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US2M, MRPS2B289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US3M, MRPS24C167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
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Find proteins for F1ST79 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US5M, MRPS5D [auth E]430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BS6M, MRPS6E [auth F]124Sus scrofaMutation(s): 0 
Gene Names: MRPS6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US7M, MRPS7F [auth G]242Sus scrofaMutation(s): 0 
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Entity ID: 7
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MITORIBOSOMAL PROTEIN US9M, MRPS9G [auth I]397Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US10M, MRPS10H [auth J]201Sus scrofaMutation(s): 0 
Gene Names: MRPS10
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US11M, MRPS11I [auth K]196Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US12M, MRPS12J [auth L]139Sus scrofaMutation(s): 0 
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Entity ID: 11
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MITORIBOSOMAL PROTEIN US14M, MRPS14K [auth N]128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
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Find proteins for A0A0M3KL53 (Sus scrofa)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US15M, MRPS15L [auth O]239Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BS16M, MRPS16M [auth P]135Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN US17M, MRPS17N [auth Q]130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
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Entity ID: 15
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MITORIBOSOMAL PROTEIN BS18M, MRPS18CO [auth R]143Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL19M, MRPL19P [auth T]14Sus scrofaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BS21M, MRPS21Q [auth U]87Sus scrofaMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS22, MRPS22U [auth a]360Sus scrofaMutation(s): 0 
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Entity ID: 21
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MITORIBOSOMAL PROTEIN MS23, MRPS23V [auth b]190Sus scrofaMutation(s): 0 
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Entity ID: 22
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MITORIBOSOMAL PROTEIN MS25, MRPS25W [auth c]173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
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Find proteins for A0A0M3KL55 (Sus scrofa)
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Entity ID: 23
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MITORIBOSOMAL PROTEIN MS26, MRPS26X [auth d]205Sus scrofaMutation(s): 0 
Gene Names: MRPS26
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Find proteins for F1S8A5 (Sus scrofa)
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Entity ID: 24
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MITORIBOSOMAL PROTEIN MS27, MRPS27Y [auth e]336Sus scrofaMutation(s): 0 
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Entity ID: 25
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MITORIBOSOMAL PROTEIN MS28, MRPS28Z [auth f]188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
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Find proteins for A0A0M3KL56 (Sus scrofa)
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Entity ID: 26
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MITORIBOSOMAL PROTEIN MS29, MRPS29AA [auth g]397Sus scrofaMutation(s): 0 
Gene Names: DAP3
UniProt
Find proteins for F1RLM4 (Sus scrofa)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS31, MRPS31BA [auth h]387Sus scrofaMutation(s): 0 
Gene Names: MRPS31
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Find proteins for F1RME2 (Sus scrofa)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS33, MRPS33CA [auth i]106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
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Find proteins for F1S8G3 (Sus scrofa)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS34, MRPS34DA [auth j]218Sus scrofaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS35, MRPS35EA [auth k]325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
UniProt
Find proteins for F1SG95 (Sus scrofa)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS37, MRPS37FA [auth m]118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS38, MRPS38GA [auth n]199Sus scrofaMutation(s): 0 
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Find proteins for A0A0M3KL57 (Sus scrofa)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN MS39, MRPS39HA [auth o]692Sus scrofaMutation(s): 0 
Gene Names: PTCD3
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Find proteins for K7GKS8 (Sus scrofa)
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Entity ID: 34
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MITORIBOSOMAL PROTEIN MS40, MRPS18BIA [auth p]258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
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Find proteins for Q767K8 (Sus scrofa)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
UNASSIGNED HELICESJA [auth s]16Sus scrofaMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
UNASSIGNED HELICESKA [auth z]17Sus scrofaMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
MITORIBOSOMAL 12S RRNAA 962Sus scrofa
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Entity ID: 18
MoleculeChainsLengthOrganismImage
P-SITE AND A-SITE TRNAR [auth V],
T [auth Y]
64Sus scrofa
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Entity ID: 19
MoleculeChainsLengthOrganismImage
MRNAS [auth X]13Sus scrofa
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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AG [auth g]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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CG [auth p],
YF [auth R],
ZF [auth c]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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