3J9M

Structure of the human mitochondrial ribosome (class 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ribosome. The structure of the human mitochondrial ribosome.

Amunts, A.Brown, A.Toots, J.Scheres, S.H.Ramakrishnan, V.

(2015) Science 348: 95-98

  • DOI: 10.1126/science.aaa1193
  • Primary Citation of Related Structures:  
    3J9M

  • PubMed Abstract: 
  • The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-pa ...

    The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-particle electron cryogenic microscopy. It reveals 80 extensively interconnected proteins, 36 of which are specific to mitochondria, and three ribosomal RNA molecules. The head domain of the small subunit, particularly the messenger (mRNA) channel, is highly remodeled. Many intersubunit bridges are specific to the mitoribosome, which adopts conformations involving ratcheting or rolling of the small subunit that are distinct from those seen in bacteria or eukaryotes. An intrinsic guanosine triphosphatase mediates a contact between the head and central protuberance. The structure provides a reference for analysis of mutations that cause severe pathologies and for future drug design.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
uL2mD305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 4
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uL3mE348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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Entity ID: 5
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uL4mF311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 6
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bL9mH267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 7
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uL10mI261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 8
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uL11mJ192Homo sapiensMutation(s): 0 
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Entity ID: 9
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uL13mK178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 10
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uL14mL145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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Entity ID: 11
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uL15mM296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 12
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uL16mN251Homo sapiensMutation(s): 0 
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Entity ID: 13
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bL17mO175Homo sapiensMutation(s): 0 
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uL18mP179Homo sapiensMutation(s): 0 
Gene Names: MRPL18hCG_34030
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bL19mQ292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 16
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bL20mR149Homo sapiensMutation(s): 0 
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bL21mS205Homo sapiensMutation(s): 0 
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uL22mT212Homo sapiensMutation(s): 0 
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uL23mU153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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Entity ID: 20
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uL24mV216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 21
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bL27mW148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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Entity ID: 22
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bL28mX256Homo sapiensMutation(s): 0 
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Entity ID: 23
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uL29mY250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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Entity ID: 24
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uL30mZ161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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Entity ID: 25
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bL32m0188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 26
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bL33m165Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 28
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bL35m3188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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Entity ID: 29
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bL36m4103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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Entity ID: 30
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mL375423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 31
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mL386380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 32
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mL397338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 33
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mL408206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 34
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mL419137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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mL42a142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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Entity ID: 36
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mL43b155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 37
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mL44c332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 38
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mL45d306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 39
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mL46e279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 40
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mL48f194Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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mL49g166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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mL50h158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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mL51i128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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mL52j123Homo sapiensMutation(s): 0 
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mL53k112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 46
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mL54l138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
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bL31mm128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 48
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mL63o102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 49
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mL62 (ICT1)p206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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Entity ID: 50
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mL64 (CRIF1)q222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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Entity ID: 51
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mL66 (bS18a)r196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 53
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Unknown protein/protein extensiont28Homo sapiensMutation(s): 0 
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Entity ID: 56
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uS2mAB296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
Find proteins for Q9Y399 (Homo sapiens)
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PHAROS  Q9Y399
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
uS3mAC167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
uS5mAD430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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PHAROS  P82675
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
bS6mAE125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
Find proteins for P82932 (Homo sapiens)
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PHAROS  P82932
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
uS7mAF242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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PHAROS  Q9Y2R9
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
uS9mAG396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
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PHAROS  P82933
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
uS10mAH201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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PHAROS  P82664
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
uS11mAI194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
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PHAROS  P82912
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
uS12mAJ138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
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PHAROS  O15235
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
uS14mAK128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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PHAROS  O60783
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
uS15mAL257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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PHAROS  P82914
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
bS16mAM137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
Find proteins for Q9Y3D3 (Homo sapiens)
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PHAROS  Q9Y3D3
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
uS17mAN130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
Find proteins for Q9Y2R5 (Homo sapiens)
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
mS40 (bS18b)AO258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
Find proteins for Q9Y676 (Homo sapiens)
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PHAROS  Q9Y676
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
bS18m (bS18c)AP142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
Find proteins for Q9Y3D5 (Homo sapiens)
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PHAROS  Q9Y3D5
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
bS21mAQ87Homo sapiensMutation(s): 0 
Gene Names: MRPS21RPMS21MDS016
Find proteins for P82921 (Homo sapiens)
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PHAROS  P82921
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
mS22AR360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
Find proteins for P82650 (Homo sapiens)
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PHAROS  P82650
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
mS23AS190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
Find proteins for Q9Y3D9 (Homo sapiens)
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PHAROS  Q9Y3D9
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
mS25AT173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
Find proteins for P82663 (Homo sapiens)
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PHAROS  P82663
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
mS26AU205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
Find proteins for Q9BYN8 (Homo sapiens)
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PHAROS  Q9BYN8
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
mS27AV414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
Find proteins for Q92552 (Homo sapiens)
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PHAROS  Q92552
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
bS1mAW187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
Find proteins for Q9Y2Q9 (Homo sapiens)
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PHAROS  Q9Y2Q9
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
mS29AX398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
Find proteins for P51398 (Homo sapiens)
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PHAROS  P51398
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
mS31AY395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
Find proteins for Q92665 (Homo sapiens)
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PHAROS  Q92665
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
mS33AZ106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
Find proteins for Q9Y291 (Homo sapiens)
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PHAROS  Q9Y291
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
mS34A0218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
Find proteins for P82930 (Homo sapiens)
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PHAROS  P82930
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
mS35A1323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
Find proteins for P82673 (Homo sapiens)
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PHAROS  P82673
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
mS37A2118Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
Find proteins for Q96BP2 (Homo sapiens)
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PHAROS  Q96BP2
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
mS38A3199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
Find proteins for Q9NWT8 (Homo sapiens)
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PHAROS  Q9NWT8
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
mS39A4579Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
Find proteins for Q96EY7 (Homo sapiens)
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PHAROS  Q96EY7
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
bL34m292Homo sapiensMutation(s): 0 
Gene Names: MRPL34
Find proteins for Q9BQ48 (Homo sapiens)
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PHAROS  Q9BQ48
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
mL65 (mS30)s439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
Find proteins for Q9NP92 (Homo sapiens)
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PHAROS  Q9NP92
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1559Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
mt-tRNAValB73Homo sapiens
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  • Entity ID: 54
    MoleculeChainsLengthOrganismImage
    E-site tRNAu2Homo sapiens
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    Entity ID: 55
    MoleculeChainsLengthOrganismImage
    12S rRNAAA954Homo sapiens
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GDP
    Query on GDP

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

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

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    A, AA, M, g
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.50 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2015-04-15
      Type: Initial release
    • Version 1.1: 2018-07-18
      Changes: Data collection