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.



Macromolecules

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Entity ID: 3
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uL2C [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2, CGI-22
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Entity ID: 4
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uL3D [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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uL4E [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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bL9F [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 7
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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 
Gene Names: MRPL21
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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 
Gene Names: MRPL37, MRPL2, RPML2, HSPC235
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mL38EA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38, HSPC262
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mL39FA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39, C21orf92, MRPL5, RPML5, MSTP003, PRED22
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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 
Gene Names: MRPL42, MRPL31, MRPS32, RPML31, HSPC204, PTD007
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mL43JA [auth b]155Homo sapiensMutation(s): 0 
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mL44KA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
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 
Gene Names: MRPL46, C15orf4, LIECG2
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mL48NA [auth f]211Homo sapiensMutation(s): 0 
Gene Names: MRPL48, CGI-118, HSPC290
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mL49OA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49, C11orf4, NOF1, OK/SW-cl.67
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Entity ID: 42
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mL50PA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 43
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mL51QA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51, MRP64, CDA09, HSPC241
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Entity ID: 44
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mL52RA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 45
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mL53SA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 46
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mL63TA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57, MRP63
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Entity ID: 47
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ICT1UA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58, DS1, ICT1
EC: 3.1.1.29
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Entity ID: 48
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CRIF1VA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1, MRPL59, PLINP1, PRG6
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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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Entity ID: 50
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mS30XA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30, PDCD9, BM-047
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Entity ID: 51
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unknown proteinYA [auth t]127Homo sapiensMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1,559Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
mt-tRNAValB73Homo 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

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View more in-depth experimental data
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