5AJ3

Structure of the small subunit of the mammalian mitoribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.1 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:  

  • 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 resolut ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US2M, MRPS2
B
289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
Find proteins for F1S001 (Sus scrofa)
Go to Gene View: MRPS2
Go to UniProtKB:  F1S001
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US3M, MRPS24
C
167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
Find proteins for F1ST79 (Sus scrofa)
Go to Gene View: MRPS24
Go to UniProtKB:  F1ST79
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US5M, MRPS5
E
430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
Find proteins for F1SU66 (Sus scrofa)
Go to Gene View: MRPS5
Go to UniProtKB:  F1SU66
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BS6M, MRPS6
F
124Sus scrofaMutation(s): 0 
Gene Names: MRPS6
Find proteins for I3LEJ9 (Sus scrofa)
Go to Gene View: MRPS6
Go to UniProtKB:  I3LEJ9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US7M, MRPS7
G
242N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US9M, MRPS9
I
397Sus scrofaMutation(s): 0 
Find proteins for A0A0M3KL59 (Sus scrofa)
Go to UniProtKB:  A0A0M3KL59
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US10M, MRPS10
J
201Sus scrofaMutation(s): 0 
Gene Names: MRPS10
Find proteins for F1RUU2 (Sus scrofa)
Go to Gene View: MRPS10
Go to UniProtKB:  F1RUU2
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US11M, MRPS11
K
196N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US12M, MRPS12
L
139Sus scrofaMutation(s): 0 
Gene Names: MRPS12
Find proteins for A0A0M3KL52 (Sus scrofa)
Go to Gene View: MRPS12
Go to UniProtKB:  A0A0M3KL52
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US14M, MRPS14
N
128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
Find proteins for A0A0M3KL53 (Sus scrofa)
Go to Gene View: MRPS14
Go to UniProtKB:  A0A0M3KL53
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US15M, MRPS15
O
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BS16M, MRPS16
P
135N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US17M, MRPS17
Q
130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
Find proteins for F1RIU0 (Sus scrofa)
Go to Gene View: MRPS17
Go to UniProtKB:  F1RIU0
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BS18M, MRPS18C
R
143Sus scrofaMutation(s): 0 
Gene Names: MRPS18C
Find proteins for A0A0M3KL54 (Sus scrofa)
Go to Gene View: MRPS18C
Go to UniProtKB:  A0A0M3KL54
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL19M, MRPL19
T
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BS21M, MRPS21
U
87N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS22, MRPS22
a
360N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS23, MRPS23
b
190N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS25, MRPS25
c
173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
Find proteins for A0A0M3KL55 (Sus scrofa)
Go to Gene View: MRPS25
Go to UniProtKB:  A0A0M3KL55
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS26, MRPS26
d
205Sus scrofaMutation(s): 0 
Gene Names: MRPS26
Find proteins for F1S8A5 (Sus scrofa)
Go to Gene View: MRPS26
Go to UniProtKB:  F1S8A5
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS27, MRPS27
e
336N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS28, MRPS28
f
188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
Find proteins for A0A0M3KL56 (Sus scrofa)
Go to Gene View: MRPS28
Go to UniProtKB:  A0A0M3KL56
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS29, MRPS29
g
397Sus scrofaMutation(s): 0 
Gene Names: DAP3
Find proteins for F1RLM4 (Sus scrofa)
Go to Gene View: DAP3
Go to UniProtKB:  F1RLM4
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS31, MRPS31
h
387Sus scrofaMutation(s): 0 
Gene Names: MRPS31
Find proteins for F1RME2 (Sus scrofa)
Go to Gene View: MRPS31
Go to UniProtKB:  F1RME2
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS33, MRPS33
i
106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
Find proteins for F1S8G3 (Sus scrofa)
Go to Gene View: MRPS33
Go to UniProtKB:  F1S8G3
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS34, MRPS34
j
218Sus scrofaMutation(s): 0 
Gene Names: MRPS34
Find proteins for F1RG19 (Sus scrofa)
Go to Gene View: MRPS34
Go to UniProtKB:  F1RG19
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS35, MRPS35
k
325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
Find proteins for F1SG95 (Sus scrofa)
Go to Gene View: MRPS35
Go to UniProtKB:  F1SG95
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS37, MRPS37
m
118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
Find proteins for F1SU49 (Sus scrofa)
Go to Gene View: CHCHD1
Go to UniProtKB:  F1SU49
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS38, MRPS38
n
199Sus scrofaMutation(s): 0 
Find proteins for A0A0M3KL57 (Sus scrofa)
Go to UniProtKB:  A0A0M3KL57
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS39, MRPS39
o
692Sus scrofaMutation(s): 0 
Gene Names: PTCD3
Find proteins for K7GKS8 (Sus scrofa)
Go to Gene View: PTCD3
Go to UniProtKB:  K7GKS8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS40, MRPS18B
p
258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
Find proteins for Q767K8 (Sus scrofa)
Go to Gene View: MRPS18B
Go to UniProtKB:  Q767K8
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
UNASSIGNED HELICES
s
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
UNASSIGNED HELICES
z
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
MITORIBOSOMAL 12S RRNAA962Sus scrofa
Entity ID: 18
MoleculeChainsLengthOrganism
P-SITE AND A-SITE TRNAV,Y64Sus scrofa
Entity ID: 19
MoleculeChainsLengthOrganism
MRNAX13Sus scrofa
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
g
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
c, p, R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, g
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
Y5P
Query on Y5P
V, X, Y
RNA LINKINGC9 H15 N2 O7 P

--

P5P
Query on P5P
V, Y
RNA LINKINGC10 H13 N4 O7 PA
UNK
Query on UNK
a, e, g, I, j, o, s, T, z
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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