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- EMDB-72525: Negative Stain EM map of KSHV glycoprotein gHgL in complex with M... -

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Basic information

Entry
Database: EMDB / ID: EMD-72525
TitleNegative Stain EM map of KSHV glycoprotein gHgL in complex with MLKH5 , MLKH10 and MLKH12 FABs.
Map data
Sample
  • Complex: Heterodimer gh/gL in complex 1:1 with MLKH3, MLKH5 and MLKH12 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: MLKH3 Heavy Chain
    • Protein or peptide: MLKH3 Light Chain
    • Protein or peptide: MLKH12 Heavy Chain
    • Protein or peptide: MLKH12 Light Chain
KeywordsKSHV / Glycoprotein / Antibody / 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: 23.07 Å
AuthorsLang K / Aldridge N / 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
DepositionSep 5, 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_72525.png

Downloads & links

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Map

FileDownload / File: emd_72525.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 384 pix.
= 606.72 Å		1.58 Å/pix.
x 384 pix.
= 606.72 Å		1.58 Å/pix.
x 384 pix.
= 606.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-0.85739875 - 3.8455358
Average (Standard dev.)-0.00022337865 (±0.059334926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 606.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72525_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_72525_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 : Heterodimer gh/gL in complex 1:1 with MLKH3, MLKH5 and MLKH12 FABs

EntireName: Heterodimer gh/gL in complex 1:1 with MLKH3, MLKH5 and MLKH12 FABs
Components
  • Complex: Heterodimer gh/gL in complex 1:1 with MLKH3, MLKH5 and MLKH12 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: MLKH3 Heavy Chain
    • Protein or peptide: MLKH3 Light Chain
    • Protein or peptide: MLKH12 Heavy Chain
    • Protein or peptide: MLKH12 Light Chain

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Supramolecule #1: Heterodimer gh/gL in complex 1:1 with MLKH3, MLKH5 and MLKH12 FABs

SupramoleculeName: Heterodimer gh/gL in complex 1:1 with MLKH3, MLKH5 and MLKH12 FABs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 244.6 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 HHHGLNDIFE AQKIEWHE

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: QVQLVESGGG VVQPGRSLRL SCAASGFIFS SYGMHWVRQA PGKGLEWIAI IWYDGSHKYY ADSVKGRFTI SRDNSKNTL YLQMNSLRAE DTAVYYCARD PGYCSRYTCY GGWFDPWGQG TLVTVSSAST KGPSVFPLAP S SKSTSGGT AALGCLVKDY FPEPVTVSWN ...String:
QVQLVESGGG VVQPGRSLRL SCAASGFIFS SYGMHWVRQA PGKGLEWIAI IWYDGSHKYY ADSVKGRFTI SRDNSKNTL YLQMNSLRAE DTAVYYCARD PGYCSRYTCY GGWFDPWGQG TLVTVSSAST KGPSVFPLAP S SKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CN VNHKP

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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: DIQMTQSPSS LSASVGDRVT ITCRASQNIN NYLNWYQQKP GKAPKVLIYA ASSLQSGVPS RFSGSGSGTD FTLTINSLQ PEDFATYYCQ RSSNSPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW KVDNALQSGN SQESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQNIN NYLNWYQQKP GKAPKVLIYA ASSLQSGVPS RFSGSGSGTD FTLTINSLQ PEDFATYYCQ RSSNSPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FN RGEC

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Macromolecule #5: MLKH3 Heavy Chain

MacromoleculeName: MLKH3 Heavy Chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG VVRPGGSLRL SCAASGFTFD DYGMSWVRQS PGKGLEWVSG INWNGGSLSY ADSIQGRFTI SRDNAENSL YLQMHSLRAE DTALYYCARV QGSGSYNNFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST S GGTAALGC LVKDYFPEPV TVSWNSGALT ...String:
EVQLLESGGG VVRPGGSLRL SCAASGFTFD DYGMSWVRQS PGKGLEWVSG INWNGGSLSY ADSIQGRFTI SRDNAENSL YLQMHSLRAE DTALYYCARV QGSGSYNNFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST S GGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KP

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Macromolecule #6: MLKH3 Light Chain

MacromoleculeName: MLKH3 Light Chain / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPDS LSVSLGERAT INCKSSQSVL YSSNNKNYLA WYQQKPGQPP KLLIYWASTR GSGVPDRFSG SGSGTDFTL TISSLQAEDV AVYYCQQYYN SPRFGGWTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC L LNNFYPRE AKVQWKVDNA LQSGNSQESV ...String:
DIVMTQSPDS LSVSLGERAT INCKSSQSVL YSSNNKNYLA WYQQKPGQPP KLLIYWASTR GSGVPDRFSG SGSGTDFTL TISSLQAEDV AVYYCQQYYN SPRFGGWTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC L LNNFYPRE AKVQWKVDNA LQSGNSQESV TEHDSKDSTY SLSSTLTLTK ADYEKHKVYA CEVTHRATAR PS QRASTRE SV

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Macromolecule #7: MLKH12 Heavy Chain

MacromoleculeName: MLKH12 Heavy Chain / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKPGGSLRL SCVASGLSFS DYYMGWIRQA PGKGPEWVAY ITSTSSYTNY ADSLKGRFTI SRDNAKTSLY LQMNNLRADD TAIYYCARSF GSGYYLDYWG QGTLVTVSSA STKGPSVFPL APSSKSTS G GTAALGCLVK DYFPEPVTVS WNSGALTSGV ...String:
EVQLVESGGG LVKPGGSLRL SCVASGLSFS DYYMGWIRQA PGKGPEWVAY ITSTSSYTNY ADSLKGRFTI SRDNAKTSLY LQMNNLRADD TAIYYCARSF GSGYYLDYWG QGTLVTVSSA STKGPSVFPL APSSKSTS G GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKP

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Macromolecule #8: MLKH12 Light Chain

MacromoleculeName: MLKH12 Light Chain / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPDS LAVSLGERAT ISCKSSQTVL HISNSKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLQAEDVA VYYCQQYYDI AWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC L LNNFYPRE AKVQWKVDNA LQSGNSQESV ...String:
EIVLTQSPDS LAVSLGERAT ISCKSSQTVL HISNSKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLQAEDVA VYYCQQYYDI AWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC L LNNFYPRE AKVQWKVDNA LQSGNSQESV TEHDSKDSTY SLSSTLTLTK ADYEKHKVYA CEVTHRATAR PS QRASTRE SV

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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
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

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 2756
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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