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- EMDB-73789: Cryo-EM structure of KSHV glycoprotein gHgL in complex with MLKH3... -

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Basic information

Entry
Database: EMDB / ID: EMD-73789
TitleCryo-EM structure of KSHV glycoprotein gHgL in complex with MLKH3 and MLKH10 FABs
Map data
Sample
  • Complex: KSHV glycoprotein heterodimer gHgL 1:1 MLKH3 and MLKH10 FABs
    • Protein or peptide: MLKH10 Light chain FV
    • Protein or peptide: MLKH10 Heavy chain FV
    • Protein or peptide: MLKH3 Light chain FV
    • Protein or peptide: MLKH3 Heavy chain FV
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
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 speciesHomo sapiens (human) / Mus musculus (house mouse) / Human gammaherpesvirus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 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: PLoS Pathog / Year: 2026
Title: Monoclonal neutralizing antibodies elicited by infection with Kaposi sarcoma-associated herpesvirus reveal critical sites of vulnerability on gH/gL.
Authors: Yu-Hsin Wan / Sara Pernikoff / Nicholas T Aldridge / Kevin Lang / Holly M Dudley / Samuel C Scharffenberger / Gargi Kher / Warren Phipps / Marie Pancera / Jim Boonyaratanakornkit / Andrew T McGuire /
Abstract: Kaposi sarcoma-associated herpesvirus (KSHV) is an oncogenic virus that causes Kaposi sarcoma, primary effusion lymphoma and multicentric Castleman disease. A vaccine that prevents KSHV infection or ...Kaposi sarcoma-associated herpesvirus (KSHV) is an oncogenic virus that causes Kaposi sarcoma, primary effusion lymphoma and multicentric Castleman disease. A vaccine that prevents KSHV infection or serves in the treatment of KSHV-related diseases represents a critical unmet need, however, the types of immune responses a vaccine should elicit have not been well defined. The gH/gL glycoprotein complex is an important target of KSHV-neutralizing antibodies, but the epitope specificities targeted by these antibodies remain unknown. Here, we isolated 12 gH/gL-specific monoclonal antibodies (mAbs) from KSHV-infected donors and performed structure/function analyses. These mAbs bind recombinant gH/gL with nanomolar affinities and epitope binning analyses revealed that the mAbs bind to 5 epitope clusters on gH/gL. Seven mAbs were able to neutralize KSHV infection of epithelial cell lines. Two potent neutralizing mAbs mapped to the EphA2 binding site as determined by inhibition of the receptor-ligand interaction and negative stain electron microscopy (nsEM) of the mAb/gH/gL complex. The epitopes of other neutralizing mAbs targeting novel sites of vulnerability were determined by a combination of cryogenic electron microscopy and nsEM. Together, these mAbs help to define the relevant epitope targets for KSHV vaccine design, have utility in understanding the role of antibodies in preventing KSHV infection, enable the development of immunotherapy approaches, and provide valuable tools to understand the molecular details of the KSHV entry process.
History
DepositionNov 7, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73789.png

Downloads & links

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Map

FileDownload / File: emd_73789.map.gz / Format: CCP4 / Size: 37.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 213 pix.
= 238.986 Å		1.12 Å/pix.
x 214 pix.
= 240.108 Å		1.12 Å/pix.
x 214 pix.
= 240.108 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.658
Minimum - Maximum-3.3517277 - 5.91778
Average (Standard dev.)-0.00092018285 (±0.1808824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions214214213
Spacing214214213
CellA: 240.108 Å / B: 240.108 Å / C: 238.986 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73789_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_73789_half_map_2.map
Projections & Slices
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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 MLKH3 and MLKH10 FABs

EntireName: KSHV glycoprotein heterodimer gHgL 1:1 MLKH3 and MLKH10 FABs
Components
  • Complex: KSHV glycoprotein heterodimer gHgL 1:1 MLKH3 and MLKH10 FABs
    • Protein or peptide: MLKH10 Light chain FV
    • Protein or peptide: MLKH10 Heavy chain FV
    • Protein or peptide: MLKH3 Light chain FV
    • Protein or peptide: MLKH3 Heavy chain FV
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L

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Supramolecule #1: KSHV glycoprotein heterodimer gHgL 1:1 MLKH3 and MLKH10 FABs

SupramoleculeName: KSHV glycoprotein heterodimer gHgL 1:1 MLKH3 and MLKH10 FABs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 184 KDa

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Macromolecule #1: MLKH10 Light chain FV

MacromoleculeName: MLKH10 Light chain FV / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.427777 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPDS LSVSLGERAT INCKSSQSVL YSSNNKNYLA WYQQKPGQPP KLLIYWASTR GSGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQYYN SPRFGGWTKV EIK

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Macromolecule #2: MLKH10 Heavy chain FV

MacromoleculeName: MLKH10 Heavy chain FV / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.144362 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGGG VVRPGGSLRL SCAASGFTFD DYGMSWVRQS PGKGLEWVSG INWNGGSLSY ADSIQGRFTI SRDNAENSLY LQMHSLRAE DTALYYCARV QGSGSYNNFD YWGQGTLVTV SS

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Macromolecule #3: MLKH3 Light chain FV

MacromoleculeName: MLKH3 Light chain FV / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.538785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQLTQSPSS VSASVGDRVT ISCRASQGIS SWLVWYQQKP GKAPKPLIYA ASSLQNGVPA RFSGSGSGTD FTLTINSLQP EDFATYYCQ QANSFPYTFG QGTKLEIK

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Macromolecule #4: MLKH3 Heavy chain FV

MacromoleculeName: MLKH3 Heavy chain FV / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.088487 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVQSGPE VKKPGSSVKV SCKASGDSFS SNTISWVRQA PGQGLEWMGR LITILGTANY AQKFQGRVTI TADETATTAY MELSSLRSE DTAIYYCAIS EGGYTYDSGS YIWGQGTLVT VSS

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Macromolecule #5: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 8 / Strain: gk18
Molecular weightTheoretical: 80.917531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSASATGAL PTTATTITRS ATQLINGRTN LSIELEFNGT SFFLNWQNLL NVITEPALTE LWTSAEVAE DLRVTLKKRQ SLFFPNKTVV ISGDGHRYTC EVPTSSQTYN ITKGFNYSAL PGHLGGFGIN ARLVLGDIFA S KWSLFARD ...String:
MDAMKRGLCC VLLLCGAVFV SPSASATGAL PTTATTITRS ATQLINGRTN LSIELEFNGT SFFLNWQNLL NVITEPALTE LWTSAEVAE DLRVTLKKRQ SLFFPNKTVV ISGDGHRYTC EVPTSSQTYN ITKGFNYSAL PGHLGGFGIN ARLVLGDIFA S KWSLFARD TPEYRVFYPM NVMAVKFSIS IGNNESGVAL YGVVSEDFVV VTLHNRSKEA NETASHLLFG LPDSLPSLKG HA TYDELTF ARNAKYALVA ILPKDSYQTL LTENYTRIFL NMTESTPLEF TRTIQTRIVS IEARRACAAQ EAAPDIFLVL FQM LVAHFL VARGIAEHRF VEVDCVCRQY AELYFLRRIS RLCMPTFTTV GYNHTTLGAV AATQIARVSA TKLASLPRSS QETV LAMVQ LGARDGAVPS SILEGIAMVV EHMYTAYTYV YTLGDTERKL MLDIHTVLTD SCPPKDSGVS EKLLRTYLMF TSMCT NIEL GEMIARFSKP DSLNIYRAFS PCFLGLRYDL HPAKLRAEAP QSSALTRTAV ARGTSGFAEL LHALHLDSLN LIPAIN CSK ITADKIIATV PLPHVTYIIS SEALSNAVVY EVSEIFLKSA MFISAIKPDC SGFNFSQIDR HIPIVYNIST PRRGCPL CD SVIMSYDESD GLQSLMYVTN ERVQTNLFLD KSPFFDNNNL HIHYLWLRDN GTVVEIRGMY GSGSGHHHHH HGLNDIFE A QKIEWHE

UniProtKB: Envelope glycoprotein H

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Macromolecule #6: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human gammaherpesvirus 8 / Strain: gk18
Molecular weightTheoretical: 18.815754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDAMKRGLCC VLLLCGAVFV SPSASDGIQY VALPCCAIQA SAASTLPLFF AVHSIHFADP NHCNGVCIAK LRSKTGDITV ETCVNGFNL RSFLVAVVRR LGSWASQENL RLLWYLQRSL TAYTVGFNAT TADSSIHNVN IIIISVGKAM NRTGSVSGSQ T RAKSSSRR AHAGQKGK

UniProtKB: Envelope glycoprotein L

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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

Concentration1 mg/mL
BufferpH: 7 / Details: 1x TBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 9372 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 19982448
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Combinaison of PDB entry for gH and gL (pdbID:7CZF) and Alphafold3 prediction for MLKH3 and MLKH10 FABs
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 75257
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainPDB ID
chain_id: A, source_name: AlphaFold, initial_model_type: in silico model
chain_id: B, source_name: AlphaFold, initial_model_type: in silico model
chain_id: C, source_name: AlphaFold, initial_model_type: in silico model
chain_id: D, source_name: AlphaFold, initial_model_type: in silico model
chain_id: E, source_name: PDB, initial_model_type: experimental model

7czf

chain_id: G, source_name: PDB, initial_model_type: experimental model

7czf

SoftwareName: UCSF ChimeraX (ver. 1.9)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9z3q:
Cryo-EM structure of KSHV glycoprotein gHgL in complex with MLKH3 and MLKH10 FABs

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