4UJC

mammalian 80S HCV-IRES initiation complex with eIF5B POST-like state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history. 


Literature

Structure of the Mammalian 80S Initiation Complex with Initiation Factor 5B on Hcv-Ires RNA.

Yamamoto, H., Unbehaun, A., Loerke, J., Behrmann, E., Collier, M., Burger, J., Mielke, T., Spahn, C.M.T.

(2014) Nat Struct Mol Biol 21: 721

  • DOI: https://doi.org/10.1038/nsmb.2859
  • Primary Citation of Related Structures:  
    4UJC, 4UJD

  • PubMed Abstract: 

    The universally conserved eukaryotic initiation factor (eIF) 5B, a translational GTPase, is essential for canonical translation initiation. It is also required for initiation facilitated by the internal ribosomal entry site (IRES) of hepatitis C virus (HCV) RNA. eIF5B promotes joining of 60S ribosomal subunits to 40S ribosomal subunits bound by initiator tRNA (Met-tRNAi(Met)). However, the exact molecular mechanism by which eIF5B acts has not been established. Here we present cryo-EM reconstructions of the mammalian 80S-HCV-IRES-Met-tRNAi(Met)-eIF5B-GMPPNP complex. We obtained two substates distinguished by the rotational state of the ribosomal subunits and the configuration of initiator tRNA in the peptidyl (P) site. Accordingly, a combination of conformational changes in the 80S ribosome and in initiator tRNA facilitates binding of the Met-tRNAi(Met) to the 60S P site and redefines the role of eIF5B as a tRNA-reorientation factor.

    • Organizational Affiliation: 

    1] Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany. [2].


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EIF5BB [auth AB]627Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TRL5 (Oryctolagus cuniculus)
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Go to UniProtKB:  G1TRL5
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UniProt GroupG1TRL5
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L8G [auth BA]257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L3H [auth BB]403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L4I [auth BC]427Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L5J [auth BD]297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L6K [auth BE]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7L [auth BF]248Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7AM [auth BG]266Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L9N [auth BH]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10O [auth BI]214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L11P [auth BJ]178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13Q [auth BL]211Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L14R [auth BM]215Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L15S [auth BN]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13AT [auth BO]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L17U [auth BP]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18V [auth BQ]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L19W [auth BR]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18AX [auth BS]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L21Y [auth BT]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L22Z [auth BU]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23AA [auth BV]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L24BA [auth BW]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23ACA [auth BX]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L26DA [auth BY]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27EA [auth BZ]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27AFA [auth Ba]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L29GA [auth Bb]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L30HA [auth Bc]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L31IA [auth Bd]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L32JA [auth Be]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L35AKA [auth Bf]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L34LA [auth Bg]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN UL29MA [auth Bh]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36NA [auth Bi]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37OA [auth Bj]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L38PA [auth Bk]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L39QA [auth Bl]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L40RA [auth Bm]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L41SA [auth Bn]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36ATA [auth Bo]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37AUA [auth Bp]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L28VA [auth Bt]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10AWA [auth Bu]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US2YA [auth CA]263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES1ZA [auth CB]264Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US5AB [auth CC]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US3BB [auth CD]243Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES4CB [auth CE]263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US7DB [auth CF]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES6EB [auth CG]249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES7FB [auth CH]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES8GB [auth CI]208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US4HB [auth CJ]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES10IB [auth CK]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US17JB [auth CL]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES12KB [auth CM]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US15LB [auth CN]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US11MB [auth CO]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US19NB [auth CP]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US9OB [auth CQ]146Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES17PB [auth CR]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US13QB [auth CS]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES19RB [auth CT]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US10SB [auth CU]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES21TB [auth CV]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US8UB [auth CW]130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US12VB [auth CX]143Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES24WB [auth CY]133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES25XB [auth CZ]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES26YB [auth Ca]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES27ZB [auth Cb]84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES28AC [auth Cc]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US14BC [auth Cd]56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES30CC [auth Ce]59Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES31DC [auth Cf]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RACK1EC [auth Cg]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
TRNAA [auth AA]76Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
HCV-IRESC [auth AC]504Hepacivirus hominis
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Entity ID: 4
MoleculeChains LengthOrganismImage
28S RIBOSOMAL RNAD [auth A2]5,025Oryctolagus cuniculus
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Entity ID: 5
MoleculeChains LengthOrganismImage
5.8S RIBOSOMAL RNAE [auth A3]194Oryctolagus cuniculus
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Entity ID: 6
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAF [auth A4]121Oryctolagus cuniculus
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Entity ID: 50
MoleculeChains LengthOrganismImage
18S RIBOSOMAL RNAXA [auth C1]1,869Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPARX
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Source and taxonomy
  • Version 2.0: 2017-08-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-12-18
    Changes: Other
  • Version 2.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary