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- EMDB-45927: KSHV glycoprotein B ectodomain, postfusion form -

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Basic information

Entry
Database: EMDB / ID: EMD-45927
TitleKSHV glycoprotein B ectodomain, postfusion form
Map data
Sample
  • Organelle or cellular component: Ectodomain of KSHV glycoprotein B in postfusion form
    • Protein or peptide: ORF8
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMembrane fusion / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma 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
Biological speciesHuman gammaherpesvirus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsIto F / Zhen J / Xie G / Huang H / Silva JC / Wu T / Zhou ZH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE025567 United States
CitationJournal: J Virol / Year: 2025
Title: Structure of the Kaposi's sarcoma-associated herpesvirus gB in post-fusion conformation.
Authors: Fumiaki Ito / James Zhen / Guodong Xie / Haigen Huang / Juan C Silva / Ting-Ting Wu / Z Hong Zhou /
Abstract: Discovered in 1994 in lesions of an AIDS patient, Kaposi's sarcoma-associated herpesvirus (KSHV) is a member of the gammaherpesvirus subfamily of the family, which contains a total of nine that ...Discovered in 1994 in lesions of an AIDS patient, Kaposi's sarcoma-associated herpesvirus (KSHV) is a member of the gammaherpesvirus subfamily of the family, which contains a total of nine that infect humans. These viruses all contain a large envelope glycoprotein, glycoprotein B (gB), that is required for viral fusion with host cell membrane to initial infection. Although the atomic structures of five other human herpesviruses in their postfusion conformation and one in its prefusion conformation are known, the atomic structure of KSHV gB has not been reported. Here, we report the first structure of the KSHV gB ectodomain determined by single-particle cryogenic electron microscopy (cryoEM). Despite a similar global fold between herpesvirus gB, KSHV gB possesses local differences not shared by its relatives in other herpesviruses. The glycosylation sites of gB are arranged in belts down the symmetry axis with distinct localization compared to that of other herpesviruses, which occludes certain antibody binding sites. An extended glycan chain observed in domain I (DI), located proximal to the host membrane, may suggest its possible role in host cell attachment. Local flexibility of domain IV (DIV) governed by molecular hinges at its interdomain junctions identifies a means for enabling conformational change. A mutation in the domain III (DIII) central helix disrupts incorporation of gB into KSHV virions despite adoption of a canonical fold . Taken together, this study reveals mechanisms of structural variability of herpesvirus fusion protein gB and informs its folding and immunogenicity.IMPORTANCEIn 1994, a cancer-causing virus was discovered in lesions of AIDS patients, which was later named Kaposi's sarcoma-associated herpesvirus (KSHV). As the latest discovered human herpesvirus, KSHV has been classified into the gammaherpesvirus subfamily of the . In this study, we have expressed KSHV gB and employed cryogenic electron microscopy (cryoEM) to determine its first structure. Importantly, our structure resolves some glycans beyond the first sugar moiety. These glycans are arranged in a pattern unique to KSHV, which impacts the antigenicity of KSHV gB. Our structure also reveals conformational flexibility caused by molecular hinges between domains that provide clues into the mechanism behind the drastic change between prefusion and postfusion states.
History
DepositionJul 25, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45927.png

Downloads & links

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Map

FileDownload / File: emd_45927.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 432 pix.
= 371.52 Å		0.86 Å/pix.
x 432 pix.
= 371.52 Å		0.86 Å/pix.
x 432 pix.
= 371.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3167681 - 0.6430623
Average (Standard dev.)0.00023441833 (±0.012082717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 371.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45927_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_45927_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ectodomain of KSHV glycoprotein B in postfusion form

EntireName: Ectodomain of KSHV glycoprotein B in postfusion form
Components
  • Organelle or cellular component: Ectodomain of KSHV glycoprotein B in postfusion form
    • Protein or peptide: ORF8
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ectodomain of KSHV glycoprotein B in postfusion form

SupramoleculeName: Ectodomain of KSHV glycoprotein B in postfusion form / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human gammaherpesvirus 8
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: ORF8

MacromoleculeName: ORF8 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 8
Molecular weightTheoretical: 71.326758 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: ASGPKSVDFY QFRVCSASIT GELFRFNLEQ TCPDTKDKYH QEGILLVYKK NIVPHIFKVR RYRKIATSVT VYRGLTESAI TNKYELPRP VPLYEISHMD STYQCFSSMK VNVNGVENTF TDRDDVNTTV FLQPVEGLTD NIQRYFSQPV IYAEPGWFPG I YRVRTTVN ...String:
ASGPKSVDFY QFRVCSASIT GELFRFNLEQ TCPDTKDKYH QEGILLVYKK NIVPHIFKVR RYRKIATSVT VYRGLTESAI TNKYELPRP VPLYEISHMD STYQCFSSMK VNVNGVENTF TDRDDVNTTV FLQPVEGLTD NIQRYFSQPV IYAEPGWFPG I YRVRTTVN CEIVDMIARS AEPYNYFVTS LGDTVEVSPF CYNESSCSTT PSNKNGLSVQ VVLNHTVVTY SDRGTSPTPQ NR IFVETGA YTLSWASESK TTAVCPLALW KTFPRSIQTT HEDSFHFVAN EITATFTAPL TPVANFTDTY SCLTSDINTT LNA SKAKLA STHVPNGTVQ YFHTTGGLYL VWQPMSAINL THAQGDRGNP TSSPPPSASP VTTSASRRKR RSASTAAAGG GGST DNLSY TQLQFAYDKL RPGINQVLEE LSRAWCREQV RDNLMWYELS KINPTSVMTA IYGRPVSAKF VGDAISVTEC INVDQ SSVN IHKSLRTNSK DVCYARPLVT FKFLNSSNLF TGQLGARNEI ILTNNQVETC KDTCEHYFIT RNETLVYKDY AYLRTI NTT DISTLNTFIA LNLSFIQNID FKAIELYSSA EKRLASSVFD LETMFREYNY YTHRLAGLRE DLDNTIDMNK E

UniProtKB: ORF8

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 14633 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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: INSILICO MODEL
In silico model: Generated by stochastic gradient descent using ab initio reconstruction in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 64516
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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