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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US2C [auth A]295Homo sapiensMutation(s): 0 
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Find proteins for P08865 (Homo sapiens)
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GTEx:  ENSG00000168028 
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UniProt GroupP08865
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES1D [auth B]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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UniProt GroupP61247
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US5E [auth C]293Homo sapiensMutation(s): 0 
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Find proteins for P15880 (Homo sapiens)
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GTEx:  ENSG00000140988 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US3F [auth D]243Homo sapiensMutation(s): 0 
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Find proteins for P23396 (Homo sapiens)
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GTEx:  ENSG00000149273 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES4G [auth E]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US7H [auth F]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES6I [auth G]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES7J [auth H]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES8K [auth I]208Homo sapiensMutation(s): 0 
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Find proteins for P62241 (Homo sapiens)
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GTEx:  ENSG00000142937 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US4L [auth J]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES10M [auth K]165Homo sapiensMutation(s): 0 
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Find proteins for P46783 (Homo sapiens)
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GTEx:  ENSG00000124614 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US17N [auth L]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES12O [auth M]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US15P [auth N]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US11Q [auth O]151Homo sapiensMutation(s): 0 
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Find proteins for P62263 (Homo sapiens)
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GTEx:  ENSG00000164587 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US19R [auth P]145Homo sapiensMutation(s): 0 
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Find proteins for P62841 (Homo sapiens)
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GTEx:  ENSG00000115268 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US9S [auth Q]146Homo sapiensMutation(s): 0 
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Find proteins for P62249 (Homo sapiens)
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GTEx:  ENSG00000105193 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES17T [auth R]135Homo sapiensMutation(s): 0 
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Find proteins for P08708 (Homo sapiens)
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GTEx:  ENSG00000182774 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US13U [auth S]152Homo sapiensMutation(s): 0 
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Find proteins for P62269 (Homo sapiens)
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GTEx:  ENSG00000231500 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES19V [auth T]146Homo sapiensMutation(s): 0 
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Find proteins for P39019 (Homo sapiens)
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GTEx:  ENSG00000105372 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US10W [auth U]119Homo sapiensMutation(s): 0 
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Find proteins for P60866 (Homo sapiens)
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GTEx:  ENSG00000008988 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES21X [auth V]83Homo sapiensMutation(s): 0 
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Find proteins for P63220 (Homo sapiens)
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GTEx:  ENSG00000171858 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US8Y [auth W]130Homo sapiensMutation(s): 0 
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Find proteins for P62244 (Homo sapiens)
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GTEx:  ENSG00000134419 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US12Z [auth X]143Homo sapiensMutation(s): 0 
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Find proteins for P62266 (Homo sapiens)
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GTEx:  ENSG00000186468 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES24AA [auth Y]130Homo sapiensMutation(s): 0 
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Find proteins for P62847 (Homo sapiens)
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GTEx:  ENSG00000138326 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES25BA [auth Z]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES26CA [auth a]101Homo sapiensMutation(s): 0 
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Find proteins for P62854 (Homo sapiens)
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GTEx:  ENSG00000197728 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES27DA [auth b]82Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES28EA [auth c]61Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN US14FA [auth d]55Homo sapiensMutation(s): 0 
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Find proteins for P62273 (Homo sapiens)
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GTEx:  ENSG00000213741 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES30GA [auth e]56Homo sapiensMutation(s): 0 
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Find proteins for P62861 (Homo sapiens)
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GTEx:  ENSG00000149806 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN ES31HA [auth f]72Homo sapiensMutation(s): 0 
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Find proteins for P62979 (Homo sapiens)
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GTEx:  ENSG00000143947 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN RACK1IA [auth g]315Homo sapiensMutation(s): 0 
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Find proteins for P63244 (Homo sapiens)
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GTEx:  ENSG00000204628 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN EL41JA [auth h]24Homo sapiensMutation(s): 0 
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Find proteins for P62945 (Homo sapiens)
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GTEx:  ENSG00000229117 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN EL19KA [auth r]13Homo sapiensMutation(s): 0 
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Find proteins for P84098 (Homo sapiens)
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GTEx:  ENSG00000108298 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN EL24LA [auth w]62Homo sapiensMutation(s): 0 
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Find proteins for P83731 (Homo sapiens)
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GTEx:  ENSG00000114391 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S RRNAA [auth 2]1,868Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
HCV IRESB [auth 3]257Hepacivirus hominis
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Small Molecules
Ligands 2 Unique
IDChains Name / 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
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2]
AC [auth 2]
AD [auth 2]
AE [auth 2]
BB [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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

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