11IQ | pdb_000011iq

Rabbit 80S with eEF2,eIF5A and SERBP1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 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: 5,454.26 kDa 
  • Atom Count: 224,491 
  • Modeled Residue Count: 18,867 
  • Deposited Residue Count: 26,066 
  • Unique protein chains: 82
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22A [auth 17]183Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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UniProt GroupG1SCJ6
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17B [auth DD]151Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth L8]248Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L3F [auth L3]394Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4G [auth L4]362Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9DCT1 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L5H [auth L5]293Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth L6]291Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7J [auth L7]253Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8K [auth aa]240Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13L [auth 13]241Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L14M [auth 14]138Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L15N [auth 15]203Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13O [auth bb]199Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TVS8 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20P [auth 20]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L21Q [auth 21]159Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22R [auth 22]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23S [auth cc]118Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26T [auth 26]134Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27U [auth 27]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aV [auth dd]147Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29W [auth 29]245Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31X [auth 31]107Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32Y [auth 32]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33Z [auth ee]109Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L34AA [auth 34]114Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXG5 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35BA [auth 35]122Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36CA [auth 36]102Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37DA [auth 37]86Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38EA [auth 38]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39FA [auth 39]50Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40GA [auth 40]52Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P0DXC2 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
eL41HA [auth 41]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
eL42IA [auth 42]104Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9D391 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aJA [auth ff]91Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28KA [auth gg]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0LA [auth s]196Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SPK4 (Oryctolagus cuniculus)
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4MA [auth EB]375Oryctolagus cuniculusMutation(s): 0 
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PHAROS:  Q9UQ80
GTEx:  ENSG00000170515 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18NA [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L10OA [auth 10]213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L9PA [auth L9]190Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7QA [auth S7]189Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S9RA [auth S9]185Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4SA [auth S4]262Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TA47 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6TA [auth S6]237Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24UA [auth SS]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S23VA [auth RR]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30WA [auth YY]55Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S18XA [auth LL]144Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L11YA [auth 11]170Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11ZA [auth GG]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14AB [auth 23]139Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L19BB [auth 19]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor 2CB [auth v]857Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.5
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PHAROS:  P13639
GTEx:  ENSG00000167658 
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S3DB [auth S3]228Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13EB [auth FF]149Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8FB [auth S8]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S2GB [auth S2]221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
40S_SA_C domain-containing proteinHB [auth BB]295Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
eS26IB [auth UU]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains  Sequence LengthOrganismDetailsImage
eS21JB [auth PP]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S17KB [auth JJ]132Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 64
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aLB [auth AS]213Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27MB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aNB [auth QQ]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24OB [auth 24]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30PB [auth 30]114Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 69
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27aQB [auth ZZ]68Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19SB [auth MM]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1TB [auth AA]313Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S20UB [auth OO]100Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChains  Sequence LengthOrganismDetailsImage
SERBP1VB [auth RB]407Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12WB [auth EE]132Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S10XB [auth CC]96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9YB [auth II]142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S25ZB [auth TT]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S28AC [auth WW]62Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S29BC [auth XX]55Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5A-1CC [auth B]149Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P10160 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal proteinDC [auth u]217Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7EC [auth S5]191Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19FC [auth A]131Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 85
MoleculeChains  Sequence LengthOrganismDetailsImage
uL11GC [auth t]153Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S rRNAC [auth 58]156Oryctolagus cuniculus
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAD [auth 5]120Oryctolagus cuniculus
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Entity ID: 70
MoleculeChains LengthOrganismImage
18S rRNARB [auth 18]1,698Oryctolagus cuniculus
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Entity ID: 86
MoleculeChains LengthOrganismImage
28S rRNAHC [auth 28]4,807Oryctolagus cuniculus
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Entity ID: 87
MoleculeChains LengthOrganismImage
ES27LIC [auth ES]5,070Oryctolagus cuniculus
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Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
DDE
Query on DDE
CB [auth v]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
5CT
Query on 5CT
CC [auth B]PEPTIDE LINKINGC10 H23 N3 O3LYS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 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