11KH | pdb_000011kh

Rabbit 80S with IFRD2 and LARP1, 40S head-swiveled


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles

Seraj, Z.Zottig, X.Huang, C.H.Loveland, A.B.Diggs, S.Sholi, E.Grigorrieff, N.Korostelev, A.A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 5,342.61 kDa 
  • Atom Count: 218,380 
  • Modeled Residue Count: 17,968 
  • Deposited Residue Count: 25,085 
  • Unique protein chains: 80
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2A [auth BB]295Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S2B [auth S2]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
eS21C [auth PP]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17D [auth DD]151Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L8G [auth L8]248Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L3H [auth L3]394Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4I [auth L4]362Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9DCT1 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L5J [auth L5]293Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P19949 (Oryctolagus cuniculus)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
large ribosomal subunit protein eL6K [auth L6]347Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7L [auth L7]225Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8M [auth aa]240Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L9N [auth L9]190Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L10O [auth 10]213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13P [auth 13]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L14Q [auth 14]138Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L15R [auth 15]203Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13S [auth bb]199Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TVS8 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L17T [auth 17]153Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L19U [auth 19]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20V [auth 20]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L21W [auth 21]159Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22X [auth 22]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23Y [auth 23]131Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23Z [auth cc]118Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26AA [auth 26]134Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27BA [auth 27]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aCA [auth dd]147Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29DA [auth 29]245Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L30EA [auth 30]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31FA [auth 31]107Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32GA [auth 32]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33HA [auth ee]109Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L34IA [auth 34]114Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXG5 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35JA [auth 35]122Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36KA [auth 36]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37LA [auth 37]86Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38MA [auth 38]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39NA [auth 39]50Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40OA [auth 40]52Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P0DXC2 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
eL41PA [auth 41]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
eL42QA [auth 42]104Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9D391 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aRA [auth ff]91Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28SA [auth gg]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aTA [auth AS]213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13UA [auth FF]149Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27VA [auth VV]83Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0WA [auth s]196Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4XA [auth F]359Oryctolagus cuniculusMutation(s): 0 
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Find proteins for Q9UQ80 (Homo sapiens)
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PHAROS:  Q9UQ80
GTEx:  ENSG00000170515 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18YA [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27aAB [auth ZZ]68Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12BB [auth EE]117Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S25CB [auth TT]75Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7DB [auth S5]191Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S28EB [auth WW]62Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9FB [auth II]142Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S10GB [auth CC]96Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1HB [auth AA]313Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S20IB [auth OO]100Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19JB [auth MM]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S18KB [auth LL]144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S15LB [auth HH]120Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S29NB [auth XX]55Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S23OB [auth RR]141Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24PB [auth SS]124Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6QB [auth S6]237Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4RB [auth S4]262Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S9SB [auth S9]185Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7TB [auth S7]189Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30UB [auth YY]55Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3VB [auth S3]214Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
UniProt
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Entity ID: 75
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S17WB [auth RS]132Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aXB [auth WX]129Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8YB [auth S8]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains  Sequence LengthOrganismDetailsImage
eL24ZB [auth W]157Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11AC [auth GG]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChains  Sequence LengthOrganismDetailsImage
eS26BC [auth UU]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L11CC [auth 11]170Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains  Sequence LengthOrganismDetailsImage
IFRD2DC [auth IF]643Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChains  Sequence LengthOrganismDetailsImage
La-related protein 1EC [auth LA]35Oryctolagus cuniculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PKG0 (Homo sapiens)
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PHAROS:  Q6PKG0
GTEx:  ENSG00000155506 
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Entity ID: 84
MoleculeChains  Sequence LengthOrganismDetailsImage
uL11FC [auth t]153Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains LengthOrganismImage
5.8S rRNAE [auth 58]156Oryctolagus cuniculus
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Entity ID: 6
MoleculeChains LengthOrganismImage
5S rRNAF [auth 5]120Oryctolagus cuniculus
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Entity ID: 52
MoleculeChains LengthOrganismImage
ES27LZA [auth ES]5,070Oryctolagus cuniculus
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Entity ID: 65
MoleculeChains LengthOrganismImage
18S rRNAMB [auth 18]1,698Oryctolagus cuniculus
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Entity ID: 85
MoleculeChains LengthOrganismImage
28S rRNAGC [auth 28]4,805Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127094

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-02
    Type: Initial release