9Q9S | pdb_00009q9s

HSV-2 prefusion glycoprotein B bound by Nb1_gbHSV


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2.

Vollmer, B.Ebel, H.Rees, R.Nentwig, J.Mulvaney, T.Schunemann, J.Krull, J.Topf, M.Gorlich, D.Grunewald, K.

(2025) Nature 646: 433-441

  • DOI: https://doi.org/10.1038/s41586-025-09438-5
  • Primary Citation of Related Structures:  
    9IH8, 9Q9L, 9Q9N, 9Q9S

  • PubMed Abstract: 

    The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein-Barr virus, present a significant burden to global public health 1 . Their envelopes contain at least ten different glycoproteins, which are necessary for host cell tropism, attachment and entry 2 . The best conserved among them, glycoprotein B (gB), is essential as it performs membrane fusion by undergoing extensive rearrangements from a prefusion to postfusion conformation. At present, there are no antiviral drugs targeting gB or neutralizing antibodies directed against its prefusion form, because of the difficulty in structurally determining and using this metastable conformation. Here we show the isolation of prefusion-specific nanobodies, one of which exhibits strong neutralizing and cross-species activity. By mutational stabilization we solved the herpes simplex virus 1 gB full-length prefusion structure, which allowed the bound epitope to be determined. Our analyses show the membrane-embedded regions of gB and previously unresolved structural features 3,4 , including a new fusion loop arrangement, providing insights into the initial conformational changes required for membrane fusion. Binding an epitope spanning three domains, proximal only in the prefusion state, the nanobody keeps wild-type HSV-2 gB in this conformation and enabled its native prefusion structure to be determined. This also indicates the mode of neutralization and an attractive avenue for antiviral interventions.


  • Organizational Affiliation
    • Centre for Structural Systems Biology (CSSB), Hamburg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nb1_gbHSVA [auth d],
B [auth e],
C [auth f]
119Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein BD [auth A],
E [auth B],
F [auth C]
948Human herpesvirus 2 strain 333Mutation(s): 0 
Gene Names: gBUL27
UniProt
Find proteins for P06763 (Human herpesvirus 2 (strain 333))
Explore P06763 
Go to UniProtKB:  P06763
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06763
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • 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
G [auth D],
H [auth E],
I [auth F],
J [auth G],
K [auth H],
G [auth D],
H [auth E],
I [auth F],
J [auth G],
K [auth H],
L [auth I],
M [auth J],
N [auth K],
O [auth L],
P [auth M],
Q [auth N],
R [auth O]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.0
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany2771, 2887
German Research Foundation (DFG)GermanyINST 152/772-1|152/774-1|152/776-1 FUGG
German Federal Ministry for Education and ResearchGermanyASPIRE
Wellcome TrustUnited Kingdom209250/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Data collection, Database references
  • Version 1.2: 2025-10-22
    Changes: Data collection, Database references