5A2Q

Structure of the HCV IRES bound to the human ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 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

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US2
A
295Homo sapiensMutation(s): 0 
Gene Names: RPSA (LAMBR, LAMR1)
Find proteins for P08865 (Homo sapiens)
Go to Gene View: RPSA
Go to UniProtKB:  P08865
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES1
B
264Homo sapiensMutation(s): 0 
Gene Names: RPS3A (FTE1, MFTL)
Find proteins for P61247 (Homo sapiens)
Go to Gene View: RPS3A
Go to UniProtKB:  P61247
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US5
C
293Homo sapiensMutation(s): 0 
Gene Names: RPS2 (RPS4)
Find proteins for P15880 (Homo sapiens)
Go to Gene View: RPS2
Go to UniProtKB:  P15880
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US3
D
243Homo sapiensMutation(s): 0 
Gene Names: RPS3
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
Go to Gene View: RPS3
Go to UniProtKB:  P23396
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES4
E
263Homo sapiensMutation(s): 0 
Gene Names: RPS4X (CCG2, RPS4, SCAR)
Find proteins for P62701 (Homo sapiens)
Go to Gene View: RPS4X
Go to UniProtKB:  P62701
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US7
F
204Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
Go to Gene View: RPS5
Go to UniProtKB:  P46782
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES6
G
249Homo sapiensMutation(s): 0 
Gene Names: RPS6
Find proteins for P62753 (Homo sapiens)
Go to Gene View: RPS6
Go to UniProtKB:  P62753
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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Go to UniProtKB:  P62081
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES8
I
208Homo sapiensMutation(s): 0 
Gene Names: RPS8
Find proteins for P62241 (Homo sapiens)
Go to Gene View: RPS8
Go to UniProtKB:  P62241
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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Go to UniProtKB:  P46781
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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Go to UniProtKB:  P46783
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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Go to UniProtKB:  P62280
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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Go to UniProtKB:  P25398
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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Go to UniProtKB:  P62277
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US11
O
151Homo sapiensMutation(s): 0 
Gene Names: RPS14
Find proteins for P62263 (Homo sapiens)
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Go to UniProtKB:  P62263
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US19
P
145Homo sapiensMutation(s): 0 
Gene Names: RPS15 (RIG)
Find proteins for P62841 (Homo sapiens)
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Go to UniProtKB:  P62841
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US9
Q
146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
Go to Gene View: RPS16
Go to UniProtKB:  P62249
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES17
R
135Homo sapiensMutation(s): 0 
Gene Names: RPS17 (RPS17L)
Find proteins for P08708 (Homo sapiens)
Go to Gene View: RPS17
Go to UniProtKB:  P08708
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US13
S
152Homo sapiensMutation(s): 0 
Gene Names: RPS18 (D6S218E)
Find proteins for P62269 (Homo sapiens)
Go to Gene View: RPS18
Go to UniProtKB:  P62269
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES19
T
146Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
Go to Gene View: RPS19
Go to UniProtKB:  P39019
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US10
U
119Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
Go to Gene View: RPS20
Go to UniProtKB:  P60866
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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Go to UniProtKB:  P63220
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN US8
W
130Homo sapiensMutation(s): 0 
Gene Names: RPS15A
Find proteins for P62244 (Homo sapiens)
Go to Gene View: RPS15A
Go to UniProtKB:  P62244
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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Go to UniProtKB:  P62266
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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Go to UniProtKB:  P62847
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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Go to UniProtKB:  P62851
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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Go to UniProtKB:  P62854
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES27
b
82Homo sapiensMutation(s): 0 
Gene Names: RPS27 (MPS1)
Find proteins for P42677 (Homo sapiens)
Go to Gene View: RPS27
Go to UniProtKB:  P42677
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES28
c
61Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
Go to Gene View: RPS28
Go to UniProtKB:  P62857
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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Go to UniProtKB:  P62273
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES30
e
56Homo sapiensMutation(s): 0 
Gene Names: FAU
Find proteins for P62861 (Homo sapiens)
Go to Gene View: FAU
Go to UniProtKB:  P62861
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN ES31
f
72Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN RACK1
g
315Homo sapiensMutation(s): 0 
Gene Names: RACK1 (GNB2L1)
Find proteins for P63244 (Homo sapiens)
Go to Gene View: RACK1
Go to UniProtKB:  P63244
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL41
h
24Homo sapiensMutation(s): 0 
Gene Names: RPL41
Find proteins for P62945 (Homo sapiens)
Go to Gene View: RPL41
Go to UniProtKB:  P62945
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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Go to UniProtKB:  P84098
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN EL24
w
62Homo sapiensMutation(s): 0 
Gene Names: RPL24
Find proteins for P83731 (Homo sapiens)
Go to Gene View: RPL24
Go to UniProtKB:  P83731
Entity ID: 1
MoleculeChainsLengthOrganism
18S RRNA21868Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
HCV IRES3257Hepacivirus C
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
2
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
w
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references
  • Version 2.0: 2017-08-02
    Type: Advisory, Atomic model, Data collection, Derived calculations, Refinement description