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: 7
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES4
E
263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
Find proteins for P62701 (Homo sapiens)
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PHAROS  P62701

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES7
H
194Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
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PHAROS  P62081

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES8
I
208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
Find proteins for P62241 (Homo sapiens)
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PHAROS  P62241

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES10
K
165Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
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PHAROS  P46783

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US15
N
151Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
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PHAROS  P62277

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US9
Q
146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
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PHAROS  P62249

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES17
R
135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
Find proteins for P08708 (Homo sapiens)
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PHAROS  P08708

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US13
S
152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
Find proteins for P62269 (Homo sapiens)
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PHAROS  P62269

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES21
V
83Homo sapiensMutation(s): 0 
Gene Names: RPS21
Find proteins for P63220 (Homo sapiens)
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PHAROS  P63220

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES24
Y
130Homo sapiensMutation(s): 0 
Gene Names: RPS24
Find proteins for P62847 (Homo sapiens)
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PHAROS  P62847

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES27
b
82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
Find proteins for P42677 (Homo sapiens)
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PHAROS  P42677

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US4
J
194Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
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PHAROS  P46781

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US17
L
158Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
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PHAROS  P62280

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES12
M
132Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
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PHAROS  P25398

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US11
O
151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
Find proteins for P62263 (Homo sapiens)
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PHAROS  P62263

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US19
P
145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
Find proteins for P62841 (Homo sapiens)
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PHAROS  P62841

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES19
T
146Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
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PHAROS  P39019

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US10
U
119Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
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PHAROS  P60866

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US8
W
130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
Find proteins for P62244 (Homo sapiens)
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PHAROS  P62244

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US12
X
143Homo sapiensMutation(s): 0 
Gene Names: RPS23
Find proteins for P62266 (Homo sapiens)
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PHAROS  P62266

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES25
Z
125Homo sapiensMutation(s): 0 
Gene Names: RPS25
Find proteins for P62851 (Homo sapiens)
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PHAROS  P62851

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES26
a
101Homo sapiensMutation(s): 0 
Gene Names: RPS26
Find proteins for P62854 (Homo sapiens)
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PHAROS  P62854

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US2
A
295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
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PHAROS  P08865

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES28
c
61Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
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PHAROS  P62857

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US14
d
55Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
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PHAROS  P62273

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES30
e
56Homo sapiensMutation(s): 0 
Gene Names: FAU
Find proteins for P62861 (Homo sapiens)
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PHAROS  P62861

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES31
f
72Homo sapiensMutation(s): 0 
Gene Names: RPS27A
Find proteins for Q5RKT7 (Homo sapiens)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN RACK1
g
315Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
Find proteins for P63244 (Homo sapiens)
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PHAROS  P63244

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL41
h
24Homo sapiensMutation(s): 0 
Gene Names: RPL41
Find proteins for P62945 (Homo sapiens)
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PHAROS  P62945
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL19
r
13Homo sapiensMutation(s): 0 
Gene Names: RPL19
Find proteins for P84098 (Homo sapiens)
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PHAROS  P84098

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL24
w
62Homo sapiensMutation(s): 0 
Gene Names: RPL24
Find proteins for P83731 (Homo sapiens)
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PHAROS  P83731

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES1
B
264Homo sapiensMutation(s): 0 
Gene Names: RPS3A
Find proteins for Q6NXR8 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US5
C
293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
Find proteins for P15880 (Homo sapiens)
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PHAROS  P15880

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US3
D
243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
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PHAROS  P23396

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US7
F
204Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES6
G
249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
Find proteins for P62753 (Homo sapiens)
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PHAROS  P62753

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Entity ID: 2
MoleculeChainsLengthOrganism
HCV IRES3257Hepacivirus C

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Entity ID: 1
MoleculeChainsLengthOrganism
18S RRNA21868Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
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

View Full Validation Report



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