6D9J

Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES.

Pisareva, V.P., Pisarev, A.V., Fernandez, I.S.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.34062
  • Primary Citation of Related Structures:  
    6D90, 6D9J

  • PubMed Abstract: 

    Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its structural genes in the late stage of infection. Ribosome hijacking is achieved by a sophisticated use of molecular mimicry to tRNA and mRNA, employed to manipulate intrinsically dynamic components of the ribosome. Binding and translocation through the ribosome is required for this IRES to initiate translation. We report two structures, solved by single particle electron cryo-microscopy (cryoEM), of a double translocated CrPV-IRES with aminoacyl-tRNA in the peptidyl site (P site) of the ribosome. CrPV-IRES adopts a previously unseen conformation, mimicking the acceptor stem of a canonical E site tRNA. The structures suggest a mechanism for the positioning of the first aminoacyl-tRNA shared with the distantly related Hepatitis C Virus IRES.

    • Organizational Affiliation: 

    Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L8257Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL3403Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L4392Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18297Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6291Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL30249Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eL8242Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1STW0 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9192Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10214Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11178Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13K [auth L]211Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPV0 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14L [auth M]198Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15M [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL13N [auth O]198Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22O [auth P]187Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL18P [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL19Q [auth R]181Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL20R [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL21S [auth T]160Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL22T [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23U [auth V]140Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL24V [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL23W [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL24X [auth Y]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27Y [auth Z]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL15Z [auth a]148Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL29AA [auth b]226Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL30BA [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eL31CA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32DA [auth e]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eL33EA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34FA [auth g]126Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL35GA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36HA [auth i]105Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37IA [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL38JA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL39KA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL40LA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL41MA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42NA [auth o]106Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eL43OA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL28PA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0QA [auth s]303Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L12RA [auth t]195Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinVA [auth K]217Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
uS2XA [auth BB]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aYA [auth CC]264Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
uS5ZA [auth DD]221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3AB [auth EE]281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
eS4BB [auth FF]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5CB [auth GG]204Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6DB [auth HH]249Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7EB [auth II]194Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8FB [auth JJ]206Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9 (Predicted)GB [auth KK]194Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
S10_plectin domain-containing proteinHB [auth LL]149Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Y5 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S11IB [auth MM]158Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12JB [auth NN]132Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S13KB [auth OO]151Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11LB [auth PP]151Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS19MB [auth QQ]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16NB [auth RR]172Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
eS17OB [auth SS]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
uS13PB [auth TT]152Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
eS19QB [auth UU]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
uS10RB [auth VV]119Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
eS21SB [auth WW]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aTB [auth XX]130Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S23UB [auth YY]143Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24VB [auth ZZ]134Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
eS25WB [auth aa]125Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
eS26XB [auth bb]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27YB [auth cc]84Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S28ZB [auth dd]69Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
eS29AC [auth ee]56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30BC [auth ff]133Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27aCC [auth gg]156Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1DC [auth hh]317Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2FC [auth 9]856Homo sapiensMutation(s): 0 
Gene Names: EEF2, EF2
EC: 3.6.5
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Find proteins for P13639 (Homo sapiens)
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PHAROS:  P13639
GTEx:  ENSG00000167658 
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Entity ID: 45
MoleculeChains LengthOrganismImage
28S rRNASA [auth 5]3,594Oryctolagus cuniculus
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Entity ID: 46
MoleculeChains LengthOrganismImage
5S rRNATA [auth 7]119Oryctolagus cuniculus
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Entity ID: 47
MoleculeChains LengthOrganismImage
5.8S rRNAUA [auth 8]151Oryctolagus cuniculus
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Entity ID: 49
MoleculeChains LengthOrganismImage
18S rRNAWA [auth 2]1,697Oryctolagus cuniculus
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Entity ID: 83
MoleculeChains LengthOrganismImage
P-site tRNAEC [auth 3]87Escherichia coli
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Entity ID: 85
MoleculeChains LengthOrganismImage
CrPV IRESGC [auth 4]190Cricket paralysis virus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2
MODEL REFINEMENTREFMAC5

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM097014

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.3: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary