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- EMDB-72130: Negative Stain EM map of KSHV glycoprotein gHgL in complex with M... -

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Basic information

Entry
Database: EMDB / ID: EMD-72130
TitleNegative Stain EM map of KSHV glycoprotein gHgL in complex with MLKH1 FAB
Map data
Sample
  • Complex: KSHV glycoprotein Heterodimer gHgl 1:1 MLKH1 FAB
    • Protein or peptide: Glycoprotein gH
    • Protein or peptide: Glycoprotein gL
    • Protein or peptide: MLKH1 FAB Ligth Chain
    • Protein or peptide: MLKH1 FAB Heavy Chain
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 / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 15.6 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_72130.png

Downloads & links

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Map

FileDownload / File: emd_72130.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: 3.39
Minimum - Maximum-6.443143 - 30.046496999999999
Average (Standard dev.)0.004144272 (±0.75218827)
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: #1

Fileemd_72130_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72130_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 Heterodimer gHgl 1:1 MLKH1 FAB

EntireName: KSHV glycoprotein Heterodimer gHgl 1:1 MLKH1 FAB
Components
  • Complex: KSHV glycoprotein Heterodimer gHgl 1:1 MLKH1 FAB
    • Protein or peptide: Glycoprotein gH
    • Protein or peptide: Glycoprotein gL
    • Protein or peptide: MLKH1 FAB Ligth Chain
    • Protein or peptide: MLKH1 FAB Heavy Chain

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Supramolecule #1: KSHV glycoprotein Heterodimer gHgl 1:1 MLKH1 FAB

SupramoleculeName: KSHV glycoprotein Heterodimer gHgl 1:1 MLKH1 FAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 145 KDa

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Macromolecule #1: Glycoprotein gH

MacromoleculeName: 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: Glycoprotein gL

MacromoleculeName: 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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Macromolecule #3: MLKH1 FAB Ligth Chain

MacromoleculeName: MLKH1 FAB Ligth Chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE IVLTQSPATL SVSPGERATL SCRASQSVSG YLAWYQQKPG QAPRLLIYAA STRATGVPG RFSGSGSGTE FTLTISSLQS EDFAVYYCQQ YTDWPPRLTF GGGTKVEIKR TVAAPSVFIF P PSDEQLKS GTASVVCLLN NFYPREAKVQ ...String:
MGWSCIILFL VATATGVHSE IVLTQSPATL SVSPGERATL SCRASQSVSG YLAWYQQKPG QAPRLLIYAA STRATGVPG RFSGSGSGTE FTLTISSLQS EDFAVYYCQQ YTDWPPRLTF GGGTKVEIKR TVAAPSVFIF P PSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KH KVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #4: MLKH1 FAB Heavy Chain

MacromoleculeName: MLKH1 FAB Heavy Chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ VQLQESGPGL VKPSQTLSLT CTVSGGSISS GDYYWNWIRQ HPVKGLEWIG YIYSSGDTH YNPSLKSRVT ISQDTSTNQF SLSLTSVTAA DTAVYYCARV NPTAAPRWYF FDSWGQGTLV A VSSASTKG PSVFPLAPSS KSTSGGTAAL ...String:
MGWSCIILFL VATATGVHSQ VQLQESGPGL VKPSQTLSLT CTVSGGSISS GDYYWNWIRQ HPVKGLEWIG YIYSSGDTH YNPSLKSRVT ISQDTSTNQF SLSLTSVTAA DTAVYYCARV NPTAAPRWYF FDSWGQGTLV A VSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SS VVTVPSS SLGTQTYICN VNHKPSNTKV DKRVEPKSCD KTHHHHHH

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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: 15.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 38778
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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