8RK0

HCV E1/E2 homodimer complex, ectodomain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

The hepatitis C virus envelope protein complex is a dimer of heterodimers.

Augestad, E.H.Holmboe Olesen, C.Gronberg, C.Soerensen, A.Velazquez-Moctezuma, R.Fanalista, M.Bukh, J.Wang, K.Gourdon, P.Prentoe, J.

(2024) Nature 633: 704-709

  • DOI: https://doi.org/10.1038/s41586-024-07783-5
  • Primary Citation of Related Structures:  
    8RJJ, 8RK0

  • PubMed Abstract: 

    Fifty-eight million individuals worldwide are affected by chronic hepatitis C virus (HCV) infection, a primary driver of liver cancer for which no vaccine is available 1 . The HCV envelope proteins E1 and E2 form a heterodimer (E1/E2), which is the target for neutralizing antibodies 2 . However, the higher-order organization of these E1/E2 heterodimers, as well as that of any Hepacivirus envelope protein complex, remains unknown. Here we determined the cryo-electron microscopy structure of two E1/E2 heterodimers in a homodimeric arrangement. We reveal how the homodimer is established at the molecular level and provide insights into neutralizing antibody evasion and membrane fusion by HCV, as orchestrated by E2 motifs such as hypervariable region 1 and antigenic site 412, as well as the organization of the transmembrane helices, including two internal to E1. This study addresses long-standing questions on the higher-order oligomeric arrangement of Hepacivirus envelope proteins and provides a critical framework in the design of novel HCV vaccine antigens.


  • Organizational Affiliation

    Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark. elias.augestad@sund.ku.dk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HCV E1A [auth C],
C [auth A]
123Hepacivirus hominisMutation(s): 0 
Gene Names: E1
UniProt
Find proteins for Q81424 (Hepacivirus hominis)
Explore Q81424 
Go to UniProtKB:  Q81424
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81424
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HCV E2B [auth D],
D [auth B]
327Hepacivirus hominisMutation(s): 0 
UniProt
Find proteins for A9YFN8 (Recombinant Hepatitis C virus S52/JFH1)
Explore A9YFN8 
Go to UniProtKB:  A9YFN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9YFN8
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E [auth L],
F [auth E],
G [auth F],
H [auth G],
I [auth H],
E [auth L],
F [auth E],
G [auth F],
H [auth G],
I [auth H],
J [auth I],
K [auth J],
L [auth K],
M,
N
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O, P, Q, R, S
O, P, Q, R, S, T, U, V
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARCv 3.3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR324-2019-1375
Novo Nordisk FoundationDenmarkNNF20SA0064340

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-02
    Changes: Data collection, Database references