6P5I

Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.

Acosta-Reyes, F.Neupane, R.Frank, J.Fernandez, I.S.

(2019) EMBO J 38: e102226-e102226

  • DOI: https://doi.org/10.15252/embj.2019102226
  • Primary Citation of Related Structures:  
    6P4G, 6P4H, 6P5I, 6P5J, 6P5K, 6P5N

  • PubMed Abstract: 

    Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uS2295Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
eS1264Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uS5255Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uS3281Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eS4263Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uS7204Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eS6249Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eS7194Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eS8207Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uS4194Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eS10149Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TPV3 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uS17158Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eS12132Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uS15151Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uS11151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
uS19145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uS9172Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eS17135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uS13152Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eS19145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uS10119Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eS2183Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TM82 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS8130Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uS12143Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eS24134Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eS25AA [auth a]125Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eS26BA [auth b]115Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TFE8 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eS27CA [auth c]84Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eS28DA [auth d]69Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eS29EA [auth e]56Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eS30FA [auth f]133Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eS31GA [auth g]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1HA [auth h]317Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
uL2MA [auth AA]257Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
uL3NA [auth AB]403Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uL4OA [auth AC]392Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
uL18PA [auth AD]297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eL6QA [auth AE]291Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
uL30RA [auth AF]249Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eL8SA [auth AG]242Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1STW0 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
uL6TA [auth AH]192Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
uL16UA [auth AI]214Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
uL11VA [auth AJ]178Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
eL13WA [auth AL]211Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
L14eXA [auth AM]198Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
eL15YA [auth AN]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
uL13ZA [auth AO]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
uL22AB [auth AP]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
eL18BB [auth AQ]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
eL19CB [auth AR]196Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJR3 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
eL20DB [auth AS]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
eL21EB [auth AT]160Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
eL22FB [auth AU]128Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
uL14GB [auth AV]140Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
eL24HB [auth AW]157Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
eL23IB [auth AX]156Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uL24JB [auth AY]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
eL27KB [auth AZ]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
uL15LB [auth Aa]148Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
eL29MB [auth Ab]226Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
eL30NB [auth Ac]115Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
eL31OB [auth Ad]125Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
eL32PB [auth Ae]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
eL33QB [auth Af]110Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
eL34RB [auth Ag]126Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
eL35SB [auth Ah]123Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
eL36TB [auth Ai]105Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
eL37UB [auth Aj]97Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
eL38VB [auth Ak]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
eL39WB [auth Al]51Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
eL40XB [auth Am]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
eL41YB [auth An]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
eL42ZB [auth Ao]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
eL43AC [auth Ap]92Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
eL28BC [auth Ar]137Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
uL1CC [auth AK]217Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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