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- PDB-9uvc: Structure of MHV68 glycoprotein B -

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Basic information

Entry
Database: PDB / ID: 9uvc
TitleStructure of MHV68 glycoprotein B
ComponentsMurid herpesvirus 68 glycoprotein B
KeywordsVIRAL PROTEIN / MHV68 / gB
Biological speciesMurid gammaherpesvirus 4 (Murine herpesvirus 68)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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 9, 2025Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Murid herpesvirus 68 glycoprotein B
B: Murid herpesvirus 68 glycoprotein B
C: Murid herpesvirus 68 glycoprotein B


Theoretical massNumber of molelcules
Total (without water)224,7593
Polymers224,7593
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 Murid herpesvirus 68 glycoprotein B


Mass: 74919.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid gammaherpesvirus 4 (Murine herpesvirus 68)
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: Murid herpesvirus 68 glycoprotein B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Murid gammaherpesvirus 4 (Murine herpesvirus 68)
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 defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109332 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00111362
ELECTRON MICROSCOPYf_angle_d0.40615538
ELECTRON MICROSCOPYf_dihedral_angle_d2.0391693
ELECTRON MICROSCOPYf_chiral_restr0.0411793
ELECTRON MICROSCOPYf_plane_restr0.0022048

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