9SV8 | pdb_00009sv8

Herpes simplex virus 2 delta28-73 glycoprotein C ectodomain in complex with C3b


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Unveiling the unique interaction mechanism of herpes simplex virus 2 glycoprotein C with C3b.

Rojas Rechy, M.H.Atanasiu, D.Hook, L.M.Cairns, T.M.Saw, W.T.Cahill, A.Guo, Z.Calabrese, A.N.Ranson, N.A.Friedman, H.M.Cohen, G.H.Fontana, J.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.10.04.680448
  • Primary Citation of Related Structures:  
    9SV8

  • PubMed Abstract: 

    The complement cascade is part of the first line of defence against viral infections, and many viruses have evolved to block it. For example, glycoprotein C (gC) from Herpes Simplex Virus 1 and 2 (gC1 and gC2) facilitates infection by modulating the complement cascade through an interaction with C3b. gC is also involved in attachment and other viral processes. However, our understanding of the molecular mechanisms of gC have been limited due to the absence of a structure. AlphaFold predicts that gC contains a disordered N-terminus and three immunoglobulin-like domains. Here, we generated various gC2 constructs and demonstrated that gC2 domains 1 and 2 are necessary and sufficient to interact with C3b and block the alternative pathway. A gC2 construct lacking the N-terminus in complex with C3b was characterised by cryo-EM at 3.6 Å, providing the first structure for gC2, and revealing that the interaction is predominantly driven by gC2 domain 2 and the MG8 domain of C3b. This structure was confirmed by cross-linking mass spectrometry and by using C3b-blocking antibodies that recognised gC2 linear epitopes at the interface with C3b. Overall, the gC-C3b interaction is different from other C3b-interacting partners, providing a novel mechanism to regulate the complement cascade.


  • Organizational Affiliation
    • School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein C479Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: gCUL44
UniProt
Find proteins for P03173 (Human herpesvirus 2 (strain G))
Explore P03173 
Go to UniProtKB:  P03173
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03173
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3 beta chain645Homo sapiensMutation(s): 1 
Gene Names: C3CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3b alpha' chain915Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC4.6.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2023-149259NB-I00,
European Regional Development FundEuropean UnionPID2023-149259NB-I00
Agencia Estatal de Investigacion (AEI)SpainPID2023-149259NB-I00
Consejo Nacional de Ciencia y Tecnologia (CONACYT)Mexico773992
Engineering and Physical Sciences Research CouncilUnited KingdomEP/W524372/1
Wellcome TrustUnited Kingdom220628/Z/20/Z
Wellcome TrustUnited Kingdom221524/Z/20/Z
Wellcome TrustUnited Kingdom223810/Z/21/Z
Wolfson FoundationUnited KingdomPR/jw/md/22597

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release