6VN1

A 2.8 Angstrom Cryo-EM Structure of a Glycoprotein B-Neutralizing Antibody Complex Reveals a Critical Domain for Herpesvirus Fusion Initiation

  • Classification: VIRAL PROTEIN/IMMUNE SYSTEM
  • Organism(s): Homo sapiens, Human alphaherpesvirus 3
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-01-29 Released: 2020-07-15 
  • Deposition Author(s): Oliver, S.L.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A glycoprotein B-neutralizing antibody structure at 2.8 angstrom uncovers a critical domain for herpesvirus fusion initiation.

Oliver, S.L.Xing, Y.Chen, D.H.Roh, S.H.Pintilie, G.D.Bushnell, D.A.Sommer, M.H.Yang, E.Carfi, A.Chiu, W.Arvin, A.M.

(2020) Nat Commun 11: 4141-4141

  • DOI: https://doi.org/10.1038/s41467-020-17911-0
  • Primary Citation of Related Structures:  
    6VLK, 6VN1

  • PubMed Abstract: 

    Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies.


  • Organizational Affiliation

    Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA. sloliver@stanford.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human monoclonal antibody 93k variable light chainA [auth L],
D [auth M],
G [auth N]
106Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Human monoclonal antibody 93k variable heavy chainB [auth H],
E [auth I],
H [auth J]
128Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein BC [auth A],
F [auth B],
I [auth C]
931Human alphaherpesvirus 3Mutation(s): 0 
UniProt
Find proteins for P09257 (Varicella-zoster virus (strain Dumas))
Explore P09257 
Go to UniProtKB:  P09257
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09257
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2020-07-15 
  • Deposition Author(s): Oliver, S.L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01A102546
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429
National Institutes of Health/Office of the DirectorUnited StatesS10OD021600

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references