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 clinically useful antibiotics ...

    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.



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uL2C [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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uL3D [auth E]348Homo sapiensMutation(s): 0 
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uL4E [auth F]311Homo sapiensMutation(s): 0 
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bL9F [auth H]267Homo sapiensMutation(s): 0 
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uL10G [auth I]261Homo sapiensMutation(s): 0 
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uL11H [auth J]192Homo sapiensMutation(s): 0 
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uL13I [auth K]178Homo sapiensMutation(s): 0 
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uL14J [auth L]145Homo sapiensMutation(s): 0 
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uL15K [auth M]296Homo sapiensMutation(s): 0 
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uL16L [auth N]251Homo sapiensMutation(s): 0 
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bL17M [auth O]175Homo sapiensMutation(s): 0 
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uL18N [auth P]179Homo sapiensMutation(s): 0 
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bL19O [auth Q]292Homo sapiensMutation(s): 0 
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bL20P [auth R]149Homo sapiensMutation(s): 0 
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bL21Q [auth S]205Homo sapiensMutation(s): 0 
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uL22R [auth T]212Homo sapiensMutation(s): 0 
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uL23S [auth U]153Homo sapiensMutation(s): 0 
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uL24T [auth V]216Homo sapiensMutation(s): 0 
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bL27U [auth W]148Homo sapiensMutation(s): 0 
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bL28V [auth X]256Homo sapiensMutation(s): 0 
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uL29W [auth Y]250Homo sapiensMutation(s): 0 
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uL30X [auth Z]161Homo sapiensMutation(s): 0 
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bL32Y [auth 0]188Homo sapiensMutation(s): 0 
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bL33Z [auth 1]65Homo sapiensMutation(s): 0 
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bL34AA [auth 2]92Homo sapiensMutation(s): 0 
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bL35BA [auth 3]188Homo sapiensMutation(s): 0 
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bL36CA [auth 4]103Homo sapiensMutation(s): 0 
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mL37DA [auth 5]423Homo sapiensMutation(s): 0 
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mL38EA [auth 6]380Homo sapiensMutation(s): 0 
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mL39FA [auth 7]338Homo sapiensMutation(s): 0 
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mL40GA [auth 8]206Homo sapiensMutation(s): 0 
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mL41HA [auth 9]137Homo sapiensMutation(s): 0 
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mL42IA [auth a]142Homo sapiensMutation(s): 0 
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mL43JA [auth b]155Homo sapiensMutation(s): 0 
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mL44KA [auth c]332Homo sapiensMutation(s): 0 
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EC: 3.1.26
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mL45LA [auth d]306Homo sapiensMutation(s): 0 
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mL46MA [auth e]279Homo sapiensMutation(s): 0 
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mL48NA [auth f]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
mL49OA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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GTEx:  ENSG00000149792 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
mL50PA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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PHAROS:  Q8N5N7
GTEx:  ENSG00000136897 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
mL51QA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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GTEx:  ENSG00000111639 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
mL52RA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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GTEx:  ENSG00000172590 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
mL53SA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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GTEx:  ENSG00000204822 
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Entity ID: 46
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mL63TA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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GTEx:  ENSG00000173141 
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Entity ID: 47
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ICT1UA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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PHAROS:  Q14197
GTEx:  ENSG00000167862 
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Entity ID: 48
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CRIF1VA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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GTEx:  ENSG00000179271 
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Entity ID: 49
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bS18aWA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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GTEx:  ENSG00000096080 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
mS30XA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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GTEx:  ENSG00000112996 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
unknown proteinYA [auth t]127Homo sapiensMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA 1559Homo sapiens
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Entity ID: 2
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mt-tRNAValB 73Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A
Query on A

Download Ideal Coordinates CCD File 
ZA [auth A]ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
OD [auth 0],
PD [auth 4],
QD [auth r]
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],
BB [auth A],
BC [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NB [auth A],
NC [auth A],
ND [auth E],
OB [auth A],
OC [auth A],
PB [auth A],
PC [auth A],
QB [auth A],
QC [auth A],
RB [auth A],
RC [auth A],
SB [auth A],
SC [auth A],
TB [auth A],
TC [auth A],
UB [auth A],
UC [auth A],
VB [auth A],
VC [auth A],
WB [auth A],
WC [auth A],
XB [auth A],
XC [auth A],
YB [auth A],
YC [auth A],
ZB [auth A],
ZC [auth A]
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  (Full details and data files)

  • 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