11JJ | pdb_000011jj

Rabbit 80S with eEF2,IFRD2 and LARP1,40S-head-swiveled


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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.Grigorieff, N.Korostelev, A.A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 5,510.97 kDa 
  • Atom Count: 224,036 
  • Modeled Residue Count: 18,765 
  • Deposited Residue Count: 26,572 
  • Unique protein chains: 81
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IFRD2A [auth IF]442Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
40S_SA_C domain-containing proteinB [auth BB]217Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJH8 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S2C [auth S2]221Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for O18789 (Bos taurus)
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
eS21D [auth PP]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17E [auth DD]151Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L8H [auth L8]248Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L3I [auth L3]394Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4J [auth L4]362Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9DCT1 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L5K [auth L5]293Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L6L [auth L6]291Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7M [auth L7]225Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8N [auth aa]240Oryctolagus cuniculusMutation(s): 0 
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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
Large ribosomal subunit protein uL23Y [auth cc]118Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26Z [auth 26]134Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27AA [auth 27]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aBA [auth dd]147Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29CA [auth 29]245Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L30DA [auth 30]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31EA [auth 31]107Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32FA [auth 32]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33GA [auth ee]109Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L34HA [auth 34]114Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXG5 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35IA [auth 35]122Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36JA [auth 36]102Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37KA [auth 37]86Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38LA [auth 38]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39MA [auth 39]50Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40NA [auth 40]52Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P0DXC2 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
eL41OA [auth 41]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
eL42PA [auth 42]104Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9D391 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aQA [auth ff]91Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28RA [auth gg]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aSA [auth AS]213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13TA [auth FF]149Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27UA [auth VV]83Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0VA [auth s]196Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SPK4 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
uL11WA [auth t]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4XA [auth F]358Oryctolagus 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: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27aZA [auth ZZ]68Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12AB [auth EE]132Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S25BB [auth TT]75Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7CB [auth S5]191Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S28DB [auth WW]62Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9EB [auth II]142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S10FB [auth CC]96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1GB [auth AA]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S20HB [auth OO]100Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19IB [auth MM]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S18JB [auth LL]144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S29KB [auth XX]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S23LB [auth RR]141Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24MB [auth SS]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6NB [auth S6]237Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4OB [auth S4]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S9PB [auth S9]185Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 69
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7QB [auth S7]189Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30RB [auth YY]55Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3SB [auth S3]214Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S17TB [auth RS]132Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aUB [auth WX]129Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8VB [auth S8]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L24WB [auth W]121Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11XB [auth GG]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChains  Sequence LengthOrganismDetailsImage
eS26YB [auth UU]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L11ZB [auth 11]170Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L9AC [auth L9]190Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor 2CC [auth v]857Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.5
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Entity ID: 82
MoleculeChains  Sequence LengthOrganismDetailsImage
LARP1DC [auth LA]1,096Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19EC [auth A]121Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 86
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14HC [auth 23]139Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains LengthOrganismImage
5.8S rRNAF [auth 58]156Oryctolagus cuniculus
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Entity ID: 7
MoleculeChains LengthOrganismImage
5S rRNAG [auth 6]120Oryctolagus cuniculus
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Entity ID: 80
MoleculeChains LengthOrganismImage
18S rRNABC [auth 18]1,698Oryctolagus cuniculus
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Entity ID: 84
MoleculeChains LengthOrganismImage
ES27LFC [auth ES]5,070Oryctolagus cuniculus
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Entity ID: 85
MoleculeChains LengthOrganismImage
28S rRNAGC [auth 28]4,808Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTPHENIX2.0_5885

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