5MRC

Structure of the yeast mitochondrial ribosome - Class A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of the yeast mitochondrial ribosome.

Desai, N.Brown, A.Amunts, A.Ramakrishnan, V.

(2017) Science 355: 528-531

  • DOI: 10.1126/science.aal2415
  • Primary Citation of Related Structures:  
    5MRC, 5MRE, 5MRF

  • PubMed Abstract: 
  • Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to a ...

    Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 angstroms. The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins, including 14 without homologs in the evolutionarily related bacterial ribosome. Yeast-specific rRNA and protein elements, including the acquisition of a putatively active enzyme, give the mitoribosome a distinct architecture compared to the mammalian mitoribosome. At an expanded messenger RNA channel exit, there is a binding platform for translational activators that regulate translation in yeast but not mammalian mitochondria. The structure provides insights into the evolution and species-specific specialization of mitochondrial translation.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. ramak@mrc-lmb.cam.ac.uk.



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MoleculeChainsSequence LengthOrganismDetailsImage
mS4233255Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P47141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
mS4344321Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P10662 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
mS4455339Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P12686 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
mS4566319Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53292 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
mS4677165Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03430 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
mS4788457Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.2.4
Find proteins for P28817 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
unknown protein sequence 1cc94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
unknown protein sequence 2dd151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
21S ribosomal RNAA3296Saccharomyces cerevisiae
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Entity ID: 75
MoleculeChainsLengthOrganismImage
15S ribosomal RNAaa1649Saccharomyces cerevisiae
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Entity ID: 76
MoleculeChainsLengthOrganismImage
tRNAbb76Saccharomyces cerevisiae
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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0, W
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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3, A, BB, MM, NN, QQ, WW, aa, d
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT096570
Wellcome TrustUnited Kingdom110301/Z/15/Z
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Agouron InstituteUnited Kingdom--
Louis-Jeantet FoundationUnited Kingdom--

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.2: 2018-02-07
    Changes: Structure summary