9DD6 | pdb_00009dd6

Cryo-EM structure of neutralizing murine antibody WS.HSV-1.24 in complex with HSV-1 glycoprotein B trimer gB-Ecto.516P.531E


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Prefusion structure, evasion and neutralization of HSV-1 glycoprotein B.

Roark, R.S.Schaub, A.J.Shi, W.Wang, M.Bahna, F.A.Becker, J.E.Biju, A.Chong, S.Du, H.Guo, Y.Hong, H.Katsamba, P.S.Mannepalli, S.M.Olia, A.S.Ou, L.Rubin, S.K.Sabo, Y.Suleiman, M.Wells, M.L.Zhang, B.Cheng, C.Glasgow, A.Ho, D.D.Huang, Y.Pierson, T.C.Rawi, R.Zhou, T.Shapiro, L.Kwong, P.D.

(2025) Nat Microbiol 10: 2966-2980

  • DOI: https://doi.org/10.1038/s41564-025-02153-x
  • Primary Citation of Related Structures:  
    9DD6, 9DD7, 9DD8, 9DDA, 9DDC

  • PubMed Abstract: 

    Glycoprotein B (gB) refolds between prefusion and postfusion conformations to facilitate herpesvirus entry into host cells. However, the isolation of prefusion-specific neutralizing antibodies, effective against other viral entry machines, has been challenging. Here we describe stabilization of the prefusion gB ectodomain from herpes simplex virus 1 (HSV-1), determine ectodomain structures at 2.9- to 4.1-Å resolution using cryogenic electron microscopy (cryo-EM) and isolate a prefusion-specific gB-neutralizing antibody termed WS.HSV-1.24. Murine immunization with gB stabilized in the prefusion conformation induced high titres of antibodies binding to both prefusion and postfusion gB, but-most notably-without measurable serum neutralization. Accessibility analysis revealed iso-surface exposure, with accessible surfaces on prefusion HSV-1 gB also exposed on postfusion gB. Structural analysis suggested substantial plasticity, with regions that refolded between pre- and postfusion conformations relegated to domain interfaces with limited accessibility; indeed, WS.HSV-1.24 recognized a domain-interface refolding region to facilitate neutralization. We propose that prefusion HSV-1 gB evades neutralization by most antibodies through an iso-surface display that is coupled to structural plasticity.


  • Organizational Affiliation
    • Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein BA [auth E],
B [auth F],
C [auth G]
808Human alphaherpesvirus 1Mutation(s): 2 
Gene Names: UL27HHV1gp041
UniProt
Find proteins for P10211 (Human herpesvirus 1 (strain 17))
Explore P10211 
Go to UniProtKB:  P10211
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10211
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WS.HSV-1.24 heavy chainD [auth H],
E [auth I],
F [auth J]
218Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
WS.HSV-1.24 light chainG [auth L],
H [auth M],
I [auth N]
214Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth A],
L [auth C],
N [auth K]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
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-glucopyranoseK [auth B],
M [auth D],
O
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references