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- EMDB-38910: Structure of KSHV glycoprotein B -

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Basic information

Entry
Database: EMDB / ID: EMD-38910
TitleStructure of KSHV glycoprotein B
Map data
Sample
  • Complex: glycoprotein B
    • Protein or peptide: Envelope 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 gammaherpesvirus 8 / Human herpesvirus 8 strain GK18
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsFang XY / Sun C / Xie C / Liu Z / Zeng MS
Funding support China, 1 items
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, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38910.png

Downloads & links

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Map

FileDownload / File: emd_38910.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.086
Minimum - Maximum-0.16679929 - 0.42838722
Average (Standard dev.)0.00007486962 (±0.012767386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local map of protein bottom

Fileemd_38910_additional_1.map
Annotationlocal map of protein bottom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38910_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38910_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : glycoprotein B

EntireName: glycoprotein B
Components
  • Complex: glycoprotein B
    • Protein or peptide: Envelope glycoprotein B

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Supramolecule #1: glycoprotein B

SupramoleculeName: glycoprotein B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human gammaherpesvirus 8

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Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 8 strain GK18 / Strain: GK18
Molecular weightTheoretical: 73.137594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTPRSRLATL GTVILLVCFC AGAAHSRGDT FQTSSSPTPP GSSSKAPTKP GEEASGPKSV DFYQFRVCSA SITGELFRFN LEQTCPDTK DKYHQEGILL VYKKNIVPHI FKVRRYRKIA TSVTVYRGHR ESAITNKYEL PRPVPLYEIS HMDSTYQCFS S MKVNVNGV ...String:
MTPRSRLATL GTVILLVCFC AGAAHSRGDT FQTSSSPTPP GSSSKAPTKP GEEASGPKSV DFYQFRVCSA SITGELFRFN LEQTCPDTK DKYHQEGILL VYKKNIVPHI FKVRRYRKIA TSVTVYRGHR ESAITNKYEL PRPVPLYEIS HMDSTYQCFS S MKVNVNGV ENTFTDRDDV NTTVFLQPVE GLTDNIQRYF SQPVIYAEPG RVEATYRVRT TVNCEIVDMI ARSAEPYNYF VT SLGDTVE VSPFCYNESS CSTTPSNKNG LSVQVVLNHT VVTYSDRGTS PTPQNRIFVE TGAYTLSWAS ESKTTAVCPL ALW KTFPRS IQTTHEDSFH FVANEITATF TAPLTPVANF TDTYSCLTSD INTTLNASKA KLASTHVPNG TVQYFHTTGG LYLV WQPMS AINLTHAQGD SGNPTSSPPP SASPMTTSAS RGGSGGASTA AAGGGGSTDN LSYTQLQFAY DKLRDGINQV LEELS RAWC REQVRDNLMW YELSKINPTS VMTAIYGRPV SAKFVGDAIS VTECINVDQS SVNIHKSLRT NSKDVCYARP LVTFKF LNS SNLFTGQLGA RNEIILTNNQ VETCKDTCEH YFITRNETLV YKDYAYLRTI NTTDISTLNT FIALNLSFIQ NIDFKAI EL YSSAEKRLAS SGSHHHHHH

UniProtKB: Envelope glycoprotein B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120100
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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