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- PDB-9uy9: Macacine gammaherpesvirus 4 glycoprotein B in complex with Fab5 -

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Basic information

Entry
Database: PDB / ID: 9uy9
TitleMacacine gammaherpesvirus 4 glycoprotein B in complex with Fab5
Components
  • Fab5 H chain
  • Fab5 L chain
  • Macacine gammaherpesvirus 4 glycoprotein B
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / rhLCV / gB / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacacine gammaherpesvirus 4 (Rhesus lymphocryptovirus)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCheng, B.Z. / Fang, X.Y. / Xie, C. / Sun, C. / Liu, Z. / Zeng, M.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: Nature / Year: 2026
Title: A broadly protective antibody targeting gammaherpesvirus gB.
Authors: Cong Sun / Chu Xie / Bing-Zhen Cheng / Zi-Ying Jiang / Pei-Huang Wu / Xin-Yan Fang / Peng-Lin Li / Xian-Shu Tian / Hang Zhou / Yan-Lin Yang / Jing Wang / Sen-Fang Sui / Zheng Liu / Mu-Sheng Zeng /
Abstract: Gammaherpesvirus is a subfamily of herpesvirus, distinct phylogenetically from alphaherpesvirus and betaherpesvirus and characterized by its oncogenic subtypes, including Epstein-Barr virus and ...Gammaherpesvirus is a subfamily of herpesvirus, distinct phylogenetically from alphaherpesvirus and betaherpesvirus and characterized by its oncogenic subtypes, including Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. It broadly infects humans and other vertebrates and causes various diseases and malignancies. However, no specific antiviral agents are available for each subtype or the whole family. gB is a common fusion protein that is vital for herpesvirus infection and is an ideal target for broad vaccine development; however, a lack of structural and mechanistic understanding of gB hinders this effort. Here we report the molecular basis of broad gB binding and cross-genus virus neutralization by an antibody, Fab5. This antibody confers effective protection against authentic virus challenges in immunocompetent mice, non-human primates and humanized mice with murine, rhesus and human gammaherpesvirus. Cryo-electron microscopy structures reveal that Fab5 targets a conserved and vulnerable epitope of gammaherpesvirus gB that is antigenically exposed in both pre-fusion and post-fusion states. This finding not only demonstrates that Fab5 is a cross-genus antibody that is broadly reactive to gammaherpesvirus infection and pathogenesis progression, but also offers insights into potential common mechanisms for herpesvirus infection and facilitates the development of broad-spectrum vaccines against gammaherpesviruses.
History
DepositionMay 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macacine gammaherpesvirus 4 glycoprotein B
B: Macacine gammaherpesvirus 4 glycoprotein B
C: Macacine gammaherpesvirus 4 glycoprotein B
H: Fab5 H chain
I: Fab5 H chain
J: Fab5 H chain
L: Fab5 L chain
M: Fab5 L chain
N: Fab5 L chain


Theoretical massNumber of molelcules
Total (without water)376,5439
Polymers376,5439
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Macacine gammaherpesvirus 4 glycoprotein B


Mass: 78052.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macacine gammaherpesvirus 4 (Rhesus lymphocryptovirus)
Production host: Homo sapiens (human)
#2: Antibody Fab5 H chain


Mass: 24199.873 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Fab5 L chain


Mass: 23261.846 Da / Num. of mol.: 3
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: Structure of rhLCV glycoprotein B in complex with Fab5
Type: COMPLEX / Entity ID: #2-#3, #1 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Macacine gammaherpesvirus 4 (Rhesus lymphocryptovirus)45455
31Mus musculus (house mouse)10090
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.3
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5533

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.3.0particle selection
2PHENIXmodel refinement
5cryoSPARCv4.3.0CTF correction
10cryoSPARCv4.3.0initial Euler assignment
11cryoSPARCv4.3.0final Euler assignment
12cryoSPARCv4.3.0classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 292826
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91810 / Num. of class averages: 32 / Symmetry type: POINT

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