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 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: 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 ...

    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

    Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EIF5B AB627Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF5B
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Go to UniProtKB:  G1TRL5
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L8 BA257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L3 BB403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L4 BC427Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L5 BD297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L6 BE158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7 BF248Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7A BG266Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L9 BH192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10 BI214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L11 BJ178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13 BL211Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L14 BM215Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L15 BN204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13A BO203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L17 BP184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18 BQ188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L19 BR196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18A BS176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L21 BT160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L22 BU128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23 BV140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L24 BW157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23A BX156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L26 BY145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27 BZ136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27A Ba148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L29 Bb159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L30 Bc115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L31 Bd125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L32 Be135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L35A Bf110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L34 Bg117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN UL29 Bh123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36 Bi105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37 Bj97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L38 Bk70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L39 Bl51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L40 Bm128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L41 Bn25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36A Bo106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37A Bp92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L28 Bt137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10A Bu210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US2 CA263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES1 CB264Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US5 CC293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US3 CD243Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES4 CE263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US7 CF204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES6 CG249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES7 CH194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES8 CI208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US4 CJ194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES10 CK165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US17 CL158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES12 CM132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US15 CN151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US11 CO151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US19 CP145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US9 CQ146Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES17 CR135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US13 CS152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES19 CT145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US10 CU119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES21 CV83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US8 CW130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US12 CX143Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES24 CY133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES25 CZ125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES26 Ca115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES27 Cb84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES28 Cc69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US14 Cd56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES30 Ce59Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES31 Cf156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RACK1 Cg317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
TRNAAA76Oryctolagus cuniculus
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Entity ID: 3
MoleculeChainsLengthOrganismImage
HCV-IRESAC504Hepacivirus C
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Entity ID: 4
MoleculeChainsLengthOrganismImage
28S RIBOSOMAL RNAA25025Oryctolagus cuniculus
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Entity ID: 5
MoleculeChainsLengthOrganismImage
5.8S RIBOSOMAL RNAA3194Oryctolagus cuniculus
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Entity ID: 6
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNAA4121Oryctolagus cuniculus
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Entity ID: 50
MoleculeChainsLengthOrganismImage
18S RIBOSOMAL RNAC11869Oryctolagus cuniculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
AB
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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