9Z3Q | pdb_00009z3q

Cryo-EM structure of KSHV glycoprotein gHgL in complex with MLKH3 and MLKH10 FABs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Monoclonal neutralizing antibodies elicited by infection with Kaposi sarcoma-associated herpesvirus reveal critical sites of vulnerability on gH/gL.

Wan, Y.H.Pernikoff, S.Aldridge, N.T.Lang, K.Dudley, H.M.Scharffenberger, S.C.Kher, G.Phipps, W.Pancera, M.Boonyaratanakornkit, J.McGuire, A.T.

(2026) PLoS Pathog 22: e1013772-e1013772

  • DOI: https://doi.org/10.1371/journal.ppat.1013772
  • Primary Citation of Related Structures:  
    9Z3Q

  • PubMed 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 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.


  • Organizational Affiliation
    • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MLKH10 Light chain FV112Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MLKH10 Heavy chain FV121Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MLKH3 Light chain FV107Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MLKH3 Heavy chain FV122Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein H728Human gammaherpesvirus 8Mutation(s): 0 
Gene Names: gHORF22
UniProt
Find proteins for F5HAK9 (Human herpesvirus 8 type P (isolate GK18))
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Go to UniProtKB:  F5HAK9
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UniProt GroupF5HAK9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein L176Human gammaherpesvirus 8Mutation(s): 0 
Gene Names: gL47
UniProt
Find proteins for F5HDB7 (Human herpesvirus 8 type P (isolate GK18))
Explore F5HDB7 
Go to UniProtKB:  F5HDB7
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UniProt GroupF5HDB7
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.7.1
MODEL REFINEMENTPHENIX2.0_5793

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesU01CA295050

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references