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- PDB-8y48: Structure of KSHV glycoprotein B -

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Basic information

Entry
Database: PDB / ID: 8y48
TitleStructure of KSHV glycoprotein B
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion 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
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 8 strain GK18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsFang, X.Y. / Sun, C. / Xie, C. / Liu, Z. / Zeng, M.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Structure and Antigenicity of Kaposi's Sarcoma-Associated Herpesvirus Glycoprotein B.
Authors: Xin-Yan Fang / Cong Sun / Chu Xie / Bing-Zhen Cheng / Zheng-Zhou Lu / Ge-Xin Zhao / Sen-Fang Sui / Mu-Sheng Zeng / Zheng Liu /
Abstract: Kaposi's sarcoma-associated herpesvirus (KSHV), a member of the human γ-herpesviruses family, exhibits extensive cellular tropism and is associated with Kaposi's sarcoma and various B-cell ...Kaposi's sarcoma-associated herpesvirus (KSHV), a member of the human γ-herpesviruses family, exhibits extensive cellular tropism and is associated with Kaposi's sarcoma and various B-cell malignancies. Despite its clinical significance, no effective prophylactic vaccines or specific therapeutics are currently available to prevent or treat KSHV infection. Similar to other herpesviruses, KSHV depends on the envelope glycoprotein B (gB) for host receptor recognition and membrane fusion initiation, making gB a prime target for antiviral antibody or vaccine development. In this study, the high-resolution cryo-electron microscopy (cryo-EM) structure of KSHV gB is presented, revealing a unique trimeric conformation resembling the postfusion state observed in other herpesviruses. Additionally, the structure of the non-neutralizing monoclonal antibody 2C4 bound to KSHV gB domain IV is resolved. The comparative sequence and structure analyses reveal significant homology in neutralizing epitopes between KSHV and Epstein-Barr virus (EBV) gB, indicating a potential pathway for the development of broad-spectrum antiviral strategies. These findings provide a foundation for a deeper understanding of KSHV's infectious mechanism and pave the way for the creation of universal interventions against the human γ-herpesviruses.
History
DepositionJan 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein B
B: Envelope glycoprotein B
C: Envelope glycoprotein B


Theoretical massNumber of molelcules
Total (without water)219,4133
Polymers219,4133
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 Envelope glycoprotein B / gB


Mass: 73137.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 strain GK18 / Strain: GK18 / Gene: gB / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: F5HB81
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: glycoprotein B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human gammaherpesvirus 8
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8.3
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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120100 / Symmetry type: POINT

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