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- PDB-9jms: Cryo-EM structure of VZV gB and FAB 16F9 complex -

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Basic information

Entry
Database: PDB / ID: 9jms
TitleCryo-EM structure of VZV gB and FAB 16F9 complex
Components
  • 16F9 VH
  • 16F9 VL
  • Glycoprotein B
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Cryo-EM / VZV gB / FAB 16F9 / Herpes virus / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain
Similarity search - Domain/homology
Biological speciesHuman herpesvirus 3 (Varicella-zoster virus)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsLi, Y. / Zheng, Q. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: A broadly neutralizing antibody confers cross-genus protection against alphaherpesviruses by inhibiting gB-mediated membrane fusion.
Authors: Guosong Wang / Yu Li / Chongxin Wu / Tian Chen / Mengxuan Gui / Yue Zeng / Hui Sun / Kaiyun Chen / Xiangfeng Xi / Yanbo Yang / Yuchen Jiang / Yanan Jiang / Liqin Liu / Chengyu Yang / Jiarui ...Authors: Guosong Wang / Yu Li / Chongxin Wu / Tian Chen / Mengxuan Gui / Yue Zeng / Hui Sun / Kaiyun Chen / Xiangfeng Xi / Yanbo Yang / Yuchen Jiang / Yanan Jiang / Liqin Liu / Chengyu Yang / Jiarui Xin / Caihong Liu / Yiyi Li / Ningning Huo / Yang Huang / Lina Lin / Hai Yu / Chenghao Huang / Quan Yuan / Shaowei Li / Kegong Tian / Qingbing Zheng / Ningshao Xia / Yixin Chen /
Abstract: The global prevalence and disease burden of alphaherpesviruses infections, including human-infecting viruses such as HSV-1, HSV-2, and VZV, as well as animal-infecting viruses like PRV, BHV, CHV, and ...The global prevalence and disease burden of alphaherpesviruses infections, including human-infecting viruses such as HSV-1, HSV-2, and VZV, as well as animal-infecting viruses like PRV, BHV, CHV, and FHV, highlight the unmet need for more effective and universal antiviral strategies. However, there has been no significant progress in developing broad-spectrum interventions against herpesvirus. Here we report the identification of a broadly neutralizing antibody against alphaherpesviruses, 16F9, which targets the glycoprotein B (gB) of alphaherpesviruses and offers cross-protection against multiple viruses such as HSV-1, HSV-2, and PRV in mice. 16F9 demonstrated robust therapeutic efficacy in various female mouse models of herpesvirus diseases including PRV-induced viral encephalitis, HSV-1-induced viral encephalitis, viral keratitis, cutaneous herpes, and neonatal herpesvirus infections. High-resolution cryo-electron microscopy structures revealed that 16F9 binds a conserved site of vulnerability on Domain I of gB. The binding of 16F9 disrupts the interaction between pre-gB and gHgL complex, thereby preventing viral membrane fusion and blocking viral infection. This study provides a foundation for advancing antiviral strategies and underscores the potential of gB-targeted interventions for combating herpesvirus infections.
History
DepositionSep 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein B
B: Glycoprotein B
C: Glycoprotein B
H: 16F9 VH
L: 16F9 VL


Theoretical massNumber of molelcules
Total (without water)336,6275
Polymers336,6275
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glycoprotein B


Mass: 86208.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human) / References: UniProt: A0A2Z5BTI6
#2: Antibody 16F9 VH


Mass: 52536.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody 16F9 VL


Mass: 25464.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DSR2 H171A / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Bacillus sp. DSM 5850 (bacteria)
Source (recombinant)Organism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118987 / Symmetry type: POINT

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