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
  • Structures With Same Primary Citation

  • 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 trans ...

    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 LengthOrganismDetails
RIBOSOMAL PROTEIN US2A295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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PHAROS  P08865
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US3D243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES4E263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US7F204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES6G249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES7H194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES8I208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US4J194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES10K165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US17L158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES12M132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US15N151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US11O151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US9Q146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES17R135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES19T146Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US10U119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US8W130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US12X143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES24Y130Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES25Z125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES26a101Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES27b82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES28c61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US14d55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES30e56Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL41h24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL24w62Homo sapiensMutation(s): 0 
Gene Names: RPL24
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US19P145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US13S152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES21V83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES31f72Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN RACK1g315Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL19r13Homo sapiensMutation(s): 0 
Gene Names: RPL19
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES1B264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US5C293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 1
MoleculeChainsLengthOrganism
18S RRNA21868Homo sapiens

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Entity ID: 2
MoleculeChainsLengthOrganism
HCV IRES3257Hepacivirus C
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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a, d, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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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 

  • 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