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 1.3 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
uL2C [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL3D [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL4E [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
bL9F [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL10G [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL11H [auth J]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL13I [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL14J [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL15K [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uL16L [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
bL17M [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL18N [auth P]179Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112110 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
bL19O [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
bL20P [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
bL21Q [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL22R [auth T]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL23S [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uL24T [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
bL27U [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
bL28V [auth X]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL29W [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL30X [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
bL32Y [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
bL33Z [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
bL34AA [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
bL35BA [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
bL36CA [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
mL37DA [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mL38EA [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mL39FA [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mL40GA [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mL41HA [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
mL42IA [auth a]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mL43JA [auth b]155Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
mL44KA [auth c]332Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135900 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
mL45LA [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mL46MA [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mL48NA [auth f]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mL49OA [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mL50PA [auth h]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136897 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mL51QA [auth i]128Homo sapiensMutation(s): 0 
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Find proteins for Q4U2R6 (Homo sapiens)
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PHAROS:  Q4U2R6
GTEx:  ENSG00000111639 
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UniProt GroupQ4U2R6
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mL52RA [auth j]123Homo sapiensMutation(s): 0 
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Find proteins for Q86TS9 (Homo sapiens)
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PHAROS:  Q86TS9
GTEx:  ENSG00000172590 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mL53SA [auth k]112Homo sapiensMutation(s): 0 
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Find proteins for Q96EL3 (Homo sapiens)
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GTEx:  ENSG00000204822 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mL63TA [auth o]102Homo sapiensMutation(s): 0 
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Find proteins for Q9BQC6 (Homo sapiens)
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PHAROS:  Q9BQC6
GTEx:  ENSG00000173141 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
ICT1UA [auth p]206Homo sapiensMutation(s): 0 
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Find proteins for Q14197 (Homo sapiens)
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GTEx:  ENSG00000167862 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
CRIF1VA [auth q]222Homo sapiensMutation(s): 0 
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Find proteins for Q8TAE8 (Homo sapiens)
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PHAROS:  Q8TAE8
GTEx:  ENSG00000179271 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
bS18aWA [auth r]196Homo sapiensMutation(s): 0 
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Find proteins for Q9NVS2 (Homo sapiens)
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GTEx:  ENSG00000096080 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mS30XA [auth s]439Homo sapiensMutation(s): 0 
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Find proteins for Q9NP92 (Homo sapiens)
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GTEx:  ENSG00000112996 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
unknown proteinYA [auth t]127Homo sapiensMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,559Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
mt-tRNAVal73Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
OD [auth 0],
PD [auth 4],
QD [auth r]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2
RECONSTRUCTIONRELION

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
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations