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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: 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
DepositionNov 7, 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_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
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 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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