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- EMDB-72133: Negative Stain EM map of KSHV glycoprotein gHgL in complex with M... -

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Basic information

Entry
Database: EMDB / ID: EMD-72133
TitleNegative Stain EM map of KSHV glycoprotein gHgL in complex with MLKH5, MLKH10 and MLKH6 FABs
Map data
Sample
  • Complex: KSHV glycoprotein heterodimer gHgL 1:1 MLKH5, MLKH10 and MLKH6 FABs
    • Protein or peptide: Glycoprotein gH
    • Protein or peptide: Glycoprotein gL
    • Protein or peptide: MLKH5 heavy chain
    • Protein or peptide: MLKH5 light chain
    • Protein or peptide: MLKH6 heavy chain
    • Protein or peptide: MLKH6 light chain
    • Protein or peptide: MLKH10 heavy chain
    • Protein or peptide: MLKH10 light 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: 24.15 Å
AuthorsLang K / Aldridge NT / 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_72133.png

Downloads & links

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Map

FileDownload / File: emd_72133.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.58 Å/pix.
x 120 pix.
= 549.6 Å		4.58 Å/pix.
x 120 pix.
= 549.6 Å		4.58 Å/pix.
x 120 pix.
= 549.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.05
Minimum - Maximum-6.1814847 - 20.134663
Average (Standard dev.)0.004402709 (±0.67094815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 549.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72133_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_72133_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 MLKH5, MLKH10 and MLKH6 FABs

EntireName: KSHV glycoprotein heterodimer gHgL 1:1 MLKH5, MLKH10 and MLKH6 FABs
Components
  • Complex: KSHV glycoprotein heterodimer gHgL 1:1 MLKH5, MLKH10 and MLKH6 FABs
    • Protein or peptide: Glycoprotein gH
    • Protein or peptide: Glycoprotein gL
    • Protein or peptide: MLKH5 heavy chain
    • Protein or peptide: MLKH5 light chain
    • Protein or peptide: MLKH6 heavy chain
    • Protein or peptide: MLKH6 light chain
    • Protein or peptide: MLKH10 heavy chain
    • Protein or peptide: MLKH10 light chain

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Supramolecule #1: KSHV glycoprotein heterodimer gHgL 1:1 MLKH5, MLKH10 and MLKH6 FABs

SupramoleculeName: KSHV glycoprotein heterodimer gHgL 1:1 MLKH5, MLKH10 and MLKH6 FABs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 242 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: MLKH5 heavy chain

MacromoleculeName: MLKH5 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ VQLVESGGGV VQPGRSLRLS CAASGFIFSS YGMHWVRQAP GKGLEWIAII WYDGSHKYYA DSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARDP GYCSRYTCYG GWFDPWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTA ...String:
MGWSCIILFL VATATGVHSQ VQLVESGGGV VQPGRSLRLS CAASGFIFSS YGMHWVRQAP GKGLEWIAII WYDGSHKYYA DSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARDP GYCSRYTCYG GWFDPWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC N VNHKPHHH HHH

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Macromolecule #4: MLKH5 light chain

MacromoleculeName: MLKH5 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSD IQMTQSPSSL SASVGDRVTI TCRASQNINN YLNWYQQKPG KAPKVLIYAA SSLQSGVPSR FSGSGSGTD FTLTINSLQP EDFATYYCQR SSNSPYTFGQ GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWK ...String:
MGWSCIILFL VATATGVHSD IQMTQSPSSL SASVGDRVTI TCRASQNINN YLNWYQQKPG KAPKVLIYAA SSLQSGVPSR FSGSGSGTD FTLTINSLQP EDFATYYCQR SSNSPYTFGQ GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF N RGEC

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Macromolecule #5: MLKH6 heavy chain

MacromoleculeName: MLKH6 heavy chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ VQLQESGPGS VRPSQTLSLT CTVSGGSITS GTYYWTWIRQ PAGKGLEWIG YISSTGNTNY NPSLKSRVT MALDTSKNQF SLKLSSVTAA DTAVYHCARG RRTTGIAAAV CDSWGQGTLA TVSSASTKGP SVFPLAPSSK STSGGTAAL ...String:
MGWSCIILFL VATATGVHSQ VQLQESGPGS VRPSQTLSLT CTVSGGSITS GTYYWTWIRQ PAGKGLEWIG YISSTGNTNY NPSLKSRVT MALDTSKNQF SLKLSSVTAA DTAVYHCARG RRTTGIAAAV CDSWGQGTLA TVSSASTKGP SVFPLAPSSK STSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV N HKPHHHHH H

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Macromolecule #6: MLKH6 light chain

MacromoleculeName: MLKH6 light chain / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE IVMTQSPATL SVSPGERATL SCRASQSLTT NLAWYQQKPG QAPRLLIYAA STRATGIPAR FSGMSGSGT EFTLTISNMQ SEDFAIYYCQ QYNNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQ ...String:
MGWSCIILFL VATATGVHSE IVMTQSPATL SVSPGERATL SCRASQSLTT NLAWYQQKPG QAPRLLIYAA STRATGIPAR FSGMSGSGT EFTLTISNMQ SEDFAIYYCQ QYNNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQ WKVDNALQSG NSQESVTEED SKDSTYSLSS TLTLSKADYE KHKVYACEVT HGGLSSPVTK S FNRGE

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Macromolecule #7: MLKH10 heavy chain

MacromoleculeName: MLKH10 heavy chain / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE VQLLESGGGV VRPGGSLRLS CAASGFTFDD YGMSWVRQSP GKGLEWVSGI NWNGGSLSYA DSIQGRFTI SRDNAENSLY LQMHSLRAED TALYYCARVQ GSGSYNNFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCL ...String:
MGWSCIILFL VATATGVHSE VQLLESGGGV VRPGGSLRLS CAASGFTFDD YGMSWVRQSP GKGLEWVSGI NWNGGSLSYA DSIQGRFTI SRDNAENSLY LQMHSLRAED TALYYCARVQ GSGSYNNFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PHHHHHH

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Macromolecule #8: MLKH10 light chain

MacromoleculeName: MLKH10 light chain / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE VDIVMTQSPD SLSVSLGERA TINCKSSQSV LYSSNNKNYL AWYQQKPGQP PKLLIYWAST RGSGVPDRFS G SGSGTDFT LTISSLQAED VAVYYCQQYY NSPRFGGWTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CL LNNFYPR ...String:
MGWSCIILFL VATATGVHSE VDIVMTQSPD SLSVSLGERA TINCKSSQSV LYSSNNKNYL AWYQQKPGQP PKLLIYWAST RGSGVPDRFS G SGSGTDFT LTISSLQAED VAVYYCQQYY NSPRFGGWTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CL LNNFYPR EAKVQWKVDN ALQSGNSQES VTEHDSKDST YSLSSTLTLT KADYEKHKVY ACEVTHRATA RPS QRASTR ESV

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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: 24.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 1881
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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