3J7Y

Structure of the large ribosomal subunit from human mitochondria


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Structure of the large ribosomal subunit from human mitochondria.

Brown, A.Amunts, A.Bai, X.C.Sugimoto, Y.Edwards, P.C.Murshudov, G.Scheres, S.H.Ramakrishnan, V.

(2014) Science 346: 718-722

  • DOI: 10.1126/science.1258026
  • Primary Citation of Related Structures:  
    3J7Y

  • PubMed Abstract: 
  • Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various c ...

    Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. Using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. The structure unveils an adaptation of the exit tunnel for hydrophobic nascent peptides, extensive remodeling of the central protuberance, including recruitment of mitochondrial valine transfer RNA (tRNA(Val)) to play an integral structural role, and changes in the tRNA binding sites related to the unusual characteristics of mitochondrial tRNAs.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.



Macromolecules

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Entity ID: 3
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uL2D305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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uL3E348Homo sapiensMutation(s): 0 
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uL4F311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 6
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bL9H267Homo sapiensMutation(s): 0 
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Entity ID: 7
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uL10I261Homo sapiensMutation(s): 0 
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Entity ID: 8
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uL11J192Homo sapiensMutation(s): 0 
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uL13K178Homo sapiensMutation(s): 0 
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uL14L145Homo sapiensMutation(s): 0 
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uL15M296Homo sapiensMutation(s): 0 
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uL16N251Homo sapiensMutation(s): 0 
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bL17O175Homo sapiensMutation(s): 0 
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uL18P179Homo sapiensMutation(s): 0 
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bL19Q292Homo sapiensMutation(s): 0 
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bL20R149Homo sapiensMutation(s): 0 
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bL21S205Homo sapiensMutation(s): 0 
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uL22T212Homo sapiensMutation(s): 0 
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uL23U153Homo sapiensMutation(s): 0 
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uL24V216Homo sapiensMutation(s): 0 
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bL27W148Homo sapiensMutation(s): 0 
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bL28X256Homo sapiensMutation(s): 0 
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uL29Y250Homo sapiensMutation(s): 0 
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uL30Z161Homo sapiensMutation(s): 0 
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bL320188Homo sapiensMutation(s): 0 
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bL33165Homo sapiensMutation(s): 0 
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bL34292Homo sapiensMutation(s): 0 
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bL353188Homo sapiensMutation(s): 0 
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bL364103Homo sapiensMutation(s): 0 
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mL375423Homo sapiensMutation(s): 0 
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mL386380Homo sapiensMutation(s): 0 
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mL397338Homo sapiensMutation(s): 0 
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mL408206Homo sapiensMutation(s): 0 
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mL419137Homo sapiensMutation(s): 0 
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mL42a142Homo sapiensMutation(s): 0 
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mL43b155Homo sapiensMutation(s): 0 
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mL44c332Homo sapiensMutation(s): 0 
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EC: 3.1.26
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mL45d306Homo sapiensMutation(s): 0 
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mL46e279Homo sapiensMutation(s): 0 
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mL48f211Homo sapiensMutation(s): 0 
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mL49g166Homo sapiensMutation(s): 0 
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mL50h158Homo sapiensMutation(s): 0 
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mL51i128Homo sapiensMutation(s): 0 
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mL52j123Homo sapiensMutation(s): 0 
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mL53k112Homo sapiensMutation(s): 0 
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mL63o102Homo sapiensMutation(s): 0 
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ICT1p206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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CRIF1q222Homo sapiensMutation(s): 0 
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bS18ar196Homo sapiensMutation(s): 0 
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mS30s439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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unknown proteint127Homo sapiensMutation(s): 0 
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1559Homo sapiens
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
mt-tRNAValB73Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A
Query on A

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A
ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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0, 4, r
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection