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- EMDB-63209: Local map of interface of KSHV gB and 2C4 fab -

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Basic information

Entry
Database: EMDB / ID: EMD-63209
TitleLocal map of interface of KSHV gB and 2C4 fab
Map data
Sample
  • Complex: Complex of KSHV post-fusion gB with 2C4 Fab
KeywordsKSHV / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFang XY / Sun C / Xie C / Zeng MS / Liu Z
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 17, 2025-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63209.png

Downloads & links

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Map

FileDownload / File: emd_63209.map.gz / Format: CCP4 / Size: 343 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 448 pix.
= 383.04 Å		0.86 Å/pix.
x 448 pix.
= 383.04 Å		0.86 Å/pix.
x 448 pix.
= 383.04 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: 0.232
Minimum - Maximum-1.0890785 - 1.3535783
Average (Standard dev.)0.00037658555 (±0.020131322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 383.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: map enhanced by EMready

Fileemd_63209_additional_1.map
Annotationmap enhanced by EMready
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63209_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63209_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of KSHV post-fusion gB with 2C4 Fab

EntireName: Complex of KSHV post-fusion gB with 2C4 Fab
Components
  • Complex: Complex of KSHV post-fusion gB with 2C4 Fab

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Supramolecule #1: Complex of KSHV post-fusion gB with 2C4 Fab

SupramoleculeName: Complex of KSHV post-fusion gB with 2C4 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
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: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 339379
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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