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- EMDB-72129: Negative Stain EM map of KSHV glycoprotein gH and gL -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72129
TitleNegative Stain EM map of KSHV glycoprotein gH and gL
Map data
Sample
  • Complex: KSHV glycoprotein gH 1:1 glycoprotein gL
    • Protein or peptide: Surface Glycoprotein gH
    • Protein or peptide: Surface Glycoprotein gL
KeywordsViral protein / Complex / Antibody / KSHV / IMMUNE SYSTEM
Function / homology
Function and homology information


host cell endosome membrane / host cell Golgi apparatus / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain
Similarity search - Domain/homology
Envelope glycoprotein H / Envelope glycoprotein L
Similarity search - Component
Biological speciesHuman gammaherpesvirus 8
Methodsingle particle reconstruction / negative staining / Resolution: 7.23 Å
AuthorsKher G / Aldridge NT / Lang K / Pancera M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)U01CA295050 United States
CitationJournal: To Be Published
Title: Monoclonal neutralizing antibodies elicited by infection with Kaposi sarcoma-associated herpesvirus reveal critical sites of vulnerability on gH/gL.
Authors: Wan YH / Pernikoff S / Aldridge N / Lang K / Dudley H / Scharffenberger S / Kher G / Phipps WT / Pancera M / Boonyaratanakornkit J / McGuire AT
History
DepositionAug 14, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72129.png

Downloads & links

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Map

FileDownload / File: emd_72129.map.gz / Format: CCP4 / Size: 432.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.43 Å/pix.
x 48 pix.
= 404.48 Å		8.43 Å/pix.
x 48 pix.
= 404.48 Å		8.43 Å/pix.
x 48 pix.
= 404.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.42667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.388
Minimum - Maximum-0.74375397 - 15.03036
Average (Standard dev.)0.0029503831 (±0.25347126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions484848
Spacing484848
CellA=B=C: 404.48004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72129_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_72129_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 : KSHV glycoprotein gH 1:1 glycoprotein gL

EntireName: KSHV glycoprotein gH 1:1 glycoprotein gL
Components
  • Complex: KSHV glycoprotein gH 1:1 glycoprotein gL
    • Protein or peptide: Surface Glycoprotein gH
    • Protein or peptide: Surface Glycoprotein gL

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Supramolecule #1: KSHV glycoprotein gH 1:1 glycoprotein gL

SupramoleculeName: KSHV glycoprotein gH 1:1 glycoprotein gL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human gammaherpesvirus 8 / Strain: GK18
Molecular weightTheoretical: 94.5 KDa

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Macromolecule #1: Surface Glycoprotein gH

MacromoleculeName: Surface Glycoprotein gH / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 8 / Strain: GK18
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSASATGAL PTTATTITRS ATQLINGRTN LSIELEFNGT SFFLNWQNLL NVITEPALTE LWTSAEVAED LRVTLKKRQS LFFPNKTVVI SGDGHRYTCE VPTSSQTYNI TKGFNYSALP GHLGGFGINA RLVLGDIFAS KWSLFARDTP ...String:
MDAMKRGLCC VLLLCGAVFV SPSASATGAL PTTATTITRS ATQLINGRTN LSIELEFNGT SFFLNWQNLL NVITEPALTE LWTSAEVAED LRVTLKKRQS LFFPNKTVVI SGDGHRYTCE VPTSSQTYNI TKGFNYSALP GHLGGFGINA RLVLGDIFAS KWSLFARDTP EYRVFYPMNV MAVKFSISIG NNESGVALYG VVSEDFVVVT LHNRSKEANE TASHLLFGLP DSLPSLKGHA TYDELTFARN AKYALVAILP KDSYQTLLTE NYTRIFLNMT ESTPLEFTRT IQTRIVSIEA RRACAAQEAA PDIFLVLFQM LVAHFLVARG IAEHRFVEVD CVCRQYAELY FLRRISRLCM PTFTTVGYNH TTLGAVAATQ IARVSATKLA SLPRSSQETV LAMVQLGARD GAVPSSILEG IAMVVEHMYT AYTYVYTLGD TERKLMLDIH TVLTDSCPPK DSGVSEKLLR TYLMFTSMCT NIELGEMIAR FSKPDSLNIY RAFSPCFLGL RYDLHPAKLR AEAPQSSALT RTAVARGTSG FAELLHALHL DSLNLIPAIN CSKITADKII ATVPLPHVTY IISSEALSNA VVYEVSEIFL KSAMFISAIK PDCSGFNFSQ IDRHIPIVYN ISTPRRGCPL CDSVIMSYDE SDGLQSLMYV TNERVQTNLF LDKSPFFDNN NLHIHYLWLR DNGTVVEIRG MYGSGSGHHH HHH

UniProtKB: Envelope glycoprotein H

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Macromolecule #2: Surface Glycoprotein gL

MacromoleculeName: Surface Glycoprotein gL / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 8 / Strain: GK18
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDAMKRGLCC VLLLCGAVFV SPSASDGIQY VALPCCAIQA SAASTLPLFF AVHSIHFADP NHCNGVCIAK LRSKTGDITV ETCVNGFNLR SFLVAVVRRL GSWASQENLR LLWYLQRSLT AYTVGFNATT ADSSIHNVNI IIISVGKAMN RTGSVSGSQT RAKSSSRRAH AGQKGK

UniProtKB: Envelope glycoprotein L

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 1x TBS
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 2% Uranyl Formate

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Electron microscopy

MicroscopeTFS TALOS L120C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 11815
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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