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
  • Structures With Same Primary Citation

  • 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. ban@mol.biol.ethz.ch.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US2M, MRPS2B289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
Find proteins for F1S001 (Sus scrofa)
Explore F1S001 
Go to UniProtKB:  F1S001
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US3M, MRPS24C167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
Find proteins for F1ST79 (Sus scrofa)
Explore F1ST79 
Go to UniProtKB:  F1ST79
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US5M, MRPS5E430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
Find proteins for F1SU66 (Sus scrofa)
Explore F1SU66 
Go to UniProtKB:  F1SU66
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BS6M, MRPS6F124Sus scrofaMutation(s): 0 
Gene Names: MRPS6
Find proteins for I3LEJ9 (Sus scrofa)
Explore I3LEJ9 
Go to UniProtKB:  I3LEJ9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US7M, MRPS7G242Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US9M, MRPS9I397Sus scrofaMutation(s): 0 
Find proteins for A0A0M3KL59 (Sus scrofa)
Explore A0A0M3KL59 
Go to UniProtKB:  A0A0M3KL59
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US10M, MRPS10J201Sus scrofaMutation(s): 0 
Gene Names: MRPS10
Find proteins for F1RUU2 (Sus scrofa)
Explore F1RUU2 
Go to UniProtKB:  F1RUU2
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US12M, MRPS12L139Sus scrofaMutation(s): 0 
Find proteins for A0A0M3KL52 (Sus scrofa)
Explore A0A0M3KL52 
Go to UniProtKB:  A0A0M3KL52
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US14M, MRPS14N128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
Find proteins for A0A0M3KL53 (Sus scrofa)
Explore A0A0M3KL53 
Go to UniProtKB:  A0A0M3KL53
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US15M, MRPS15O239Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BS16M, MRPS16P135Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US17M, MRPS17Q130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
Find proteins for F1RIU0 (Sus scrofa)
Explore F1RIU0 
Go to UniProtKB:  F1RIU0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS23, MRPS23b190Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS26, MRPS26d205Sus scrofaMutation(s): 0 
Gene Names: MRPS26
Find proteins for F1S8A5 (Sus scrofa)
Explore F1S8A5 
Go to UniProtKB:  F1S8A5
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS28, MRPS28f188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
Find proteins for A0A0M3KL56 (Sus scrofa)
Explore A0A0M3KL56 
Go to UniProtKB:  A0A0M3KL56
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS29, MRPS29g397Sus scrofaMutation(s): 0 
Gene Names: DAP3
Find proteins for F1RLM4 (Sus scrofa)
Explore F1RLM4 
Go to UniProtKB:  F1RLM4
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS33, MRPS33i106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
Find proteins for F1S8G3 (Sus scrofa)
Explore F1S8G3 
Go to UniProtKB:  F1S8G3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS34, MRPS34j218Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS35, MRPS35k325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
Find proteins for F1SG95 (Sus scrofa)
Explore F1SG95 
Go to UniProtKB:  F1SG95
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS37, MRPS37m118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
Find proteins for F1SU49 (Sus scrofa)
Explore F1SU49 
Go to UniProtKB:  F1SU49
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS38, MRPS38n199Sus scrofaMutation(s): 0 
Find proteins for A0A0M3KL57 (Sus scrofa)
Explore A0A0M3KL57 
Go to UniProtKB:  A0A0M3KL57
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS39, MRPS39o692Sus scrofaMutation(s): 0 
Gene Names: PTCD3
Find proteins for K7GKS8 (Sus scrofa)
Explore K7GKS8 
Go to UniProtKB:  K7GKS8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS40, MRPS18Bp258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
Find proteins for Q767K8 (Sus scrofa)
Explore Q767K8 
Go to UniProtKB:  Q767K8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
UNASSIGNED HELICESs16Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
UNASSIGNED HELICESz17Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BS18M, MRPS18CR143Sus scrofaMutation(s): 0 
Find proteins for A0A0M3KL54 (Sus scrofa)
Explore A0A0M3KL54 
Go to UniProtKB:  A0A0M3KL54
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL19M, MRPL19T14Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BS21M, MRPS21U87Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS22, MRPS22a360Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS25, MRPS25c173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
Find proteins for A0A0M3KL55 (Sus scrofa)
Explore A0A0M3KL55 
Go to UniProtKB:  A0A0M3KL55
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS27, MRPS27e336Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN MS31, MRPS31h387Sus scrofaMutation(s): 0 
Gene Names: MRPS31
Find proteins for F1RME2 (Sus scrofa)
Explore F1RME2 
Go to UniProtKB:  F1RME2
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN US11M, MRPS11K196Sus scrofaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
MITORIBOSOMAL 12S RRNAA962Sus scrofa
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 19
MoleculeChainsLengthOrganism
MRNAX13Sus scrofa

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 18
MoleculeChainsLengthOrganism
P-SITE AND A-SITE TRNAV, Y64Sus scrofa
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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

Download CCD File 
A, g
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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