5A2Q

Structure of the HCV IRES bound to the human ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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

Cryo-Em Structure of Hepatitis C Virus Ires Bound to the Human Ribosome at 3.9 Angstrom Resolution

Quade, N.Boehringer, D.Leibundgut, M.Van Den Heuvel, J.Ban, N.

(2015) Nat Commun 6: 7646

  • DOI: 10.1038/ncomms8646
  • Primary Citation of Related Structures:  
    5A2Q

  • PubMed Abstract: 
  • Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning ...

    Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US2C [auth A]295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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Entity ID: 4
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RIBOSOMAL PROTEIN ES1D [auth B]264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 5
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RIBOSOMAL PROTEIN US5E [auth C]293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 6
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RIBOSOMAL PROTEIN US3F [auth D]243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 7
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RIBOSOMAL PROTEIN ES4G [auth E]263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 8
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RIBOSOMAL PROTEIN US7H [auth F]204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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RIBOSOMAL PROTEIN ES6I [auth G]249Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN ES7J [auth H]194Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN ES8K [auth I]208Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN US4L [auth J]194Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN ES10M [auth K]165Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN US17N [auth L]158Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN ES12O [auth M]132Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN US15P [auth N]151Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN US11Q [auth O]151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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RIBOSOMAL PROTEIN US19R [auth P]145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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RIBOSOMAL PROTEIN US9S [auth Q]146Homo sapiensMutation(s): 0 
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Entity ID: 20
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RIBOSOMAL PROTEIN ES17T [auth R]135Homo sapiensMutation(s): 0 
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RIBOSOMAL PROTEIN US13U [auth S]152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 22
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RIBOSOMAL PROTEIN ES19V [auth T]146Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 23
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RIBOSOMAL PROTEIN US10W [auth U]119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 24
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RIBOSOMAL PROTEIN ES21X [auth V]83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 25
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RIBOSOMAL PROTEIN US8Y [auth W]130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 26
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RIBOSOMAL PROTEIN US12Z [auth X]143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 27
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RIBOSOMAL PROTEIN ES24AA [auth Y]130Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 28
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RIBOSOMAL PROTEIN ES25BA [auth Z]125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 29
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RIBOSOMAL PROTEIN ES26CA [auth a]101Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 30
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RIBOSOMAL PROTEIN ES27DA [auth b]82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 31
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RIBOSOMAL PROTEIN ES28EA [auth c]61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 32
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RIBOSOMAL PROTEIN US14FA [auth d]55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 33
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RIBOSOMAL PROTEIN ES30GA [auth e]56Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 34
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RIBOSOMAL PROTEIN ES31HA [auth f]72Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 35
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RIBOSOMAL PROTEIN RACK1IA [auth g]315Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 36
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RIBOSOMAL PROTEIN EL41JA [auth h]24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 37
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RIBOSOMAL PROTEIN EL19KA [auth r]13Homo sapiensMutation(s): 0 
Gene Names: RPL19
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Entity ID: 38
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RIBOSOMAL PROTEIN EL24LA [auth w]62Homo sapiensMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S RRNAA [auth 2]1868Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
HCV IRESB [auth 3]257Hepacivirus C
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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GE [auth a], HE [auth d], IE [auth f]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth 2] , AC [auth 2] , AD [auth 2] , AE [auth 2] , BB [auth 2] , BC [auth 2] , BD [auth 2] , BE [auth 2] , 
AB [auth 2],  AC [auth 2],  AD [auth 2],  AE [auth 2],  BB [auth 2],  BC [auth 2],  BD [auth 2],  BE [auth 2],  CB [auth 2],  CC [auth 2],  CD [auth 2],  CE [auth 2],  DB [auth 2],  DC [auth 2],  DD [auth 2],  DE [auth 2],  EB [auth 2],  EC [auth 2],  ED [auth 2],  EE [auth 2],  FB [auth 2],  FC [auth 2],  FD [auth 2],  FE [auth 2],  GB [auth 2],  GC [auth 2],  GD [auth 2],  HB [auth 2],  HC [auth 2],  HD [auth 2],  IB [auth 2],  IC [auth 2],  ID [auth 2],  JB [auth 2],  JC [auth 2],  JD [auth 2],  KB [auth 2],  KC [auth 2],  KD [auth 2],  LB [auth 2],  LC [auth 2],  LD [auth 2],  MA [auth 2],  MB [auth 2],  MC [auth 2],  MD [auth 2],  NA [auth 2],  NB [auth 2],  NC [auth 2],  ND [auth 2],  OA [auth 2],  OB [auth 2],  OC [auth 2],  OD [auth 2],  PA [auth 2],  PB [auth 2],  PC [auth 2],  PD [auth 2],  QA [auth 2],  QB [auth 2],  QC [auth 2],  QD [auth 2],  RA [auth 2],  RB [auth 2],  RC [auth 2],  RD [auth 2],  SA [auth 2],  SB [auth 2],  SC [auth 2],  SD [auth 2],  TA [auth 2],  TB [auth 2],  TC [auth 2],  TD [auth 2],  UA [auth 2],  UB [auth 2],  UC [auth 2],  UD [auth 2],  VA [auth 2],  VB [auth 2],  VC [auth 2],  VD [auth 2],  WA [auth 2],  WB [auth 2],  WC [auth 2],  WD [auth 2],  XA [auth 2],  XB [auth 2],  XC [auth 2],  XD [auth 2],  YA [auth 2],  YB [auth 2],  YC [auth 2],  YD [auth 2],  ZA [auth 2],  ZB [auth 2],  ZC [auth 2],  ZD [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Database references
  • Version 2.0: 2017-08-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2019-12-18
    Changes: Derived calculations, Other