8W1A | pdb_00008w1a

Cryo-EM Structure of KSHV ORF74 Apo Dimer at 2.8A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8W1A

This is version 1.1 of the entry. See complete history

Literature

Structural basis for ligand promiscuity and high signaling activity of Kaposi's Sarcoma-associated Herpesvirus-encoded GPCR.

Park, J.B.Sahoo, B.Sahoo, A.R.Kim, D.Seo, H.D.Bowman, J.Kwak, M.J.Suh, S.Buck, M.Dai, X.Jung, J.U.

(2025) Nat Commun 16: 8403-8403

  • DOI: https://doi.org/10.1038/s41467-025-63457-4
  • Primary Citation Related Structures: 
    8W1A, 9EJC

  • PubMed Abstract: 

    Kaposi's Sarcoma-associated Herpesvirus encodes ORF74, a viral G protein-coupled receptor homologous to CXCR2, which plays a crucial role in Kaposi's Sarcoma development through its high basal signaling activity. Our cryoEM analysis of ORF74 in ligand-free, BRIL-fused ligand-free, and CXCL1/Gi trimer -bound forms elucidates its ligand-independent signaling activity. A widely open, static extracellular cavity facilitates ligand promiscuity by enabling dynamic access and diverse binding modes. Structural alterations in CWxP, E/DRY, and NPxxY micro-switches stabilize the active conformation, leading to constitutive signaling. Metadynamics simulations reveal a dynamic ensemble between local switch structures corresponding to the inactive and active states, supporting spontaneous activation. CXCR2-ORF74 chimeras highlight intracellular loops 2 and 3 as key modulators of basal and agonist-induced activity. This study defines the structural basis of ORF74's ligand promiscuity, spontaneous activation, and high basal signaling, providing insights into its role in viral oncogenesis.


  • Organizational Affiliation
    • Cancer Biology Department, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.

Macromolecule Content 

  • Total Structure Weight: 84.26 kDa 
  • Atom Count: 4,664 
  • Modeled Residue Count: 584 
  • Deposited Residue Count: 738 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
viral G-protein coupled receptor
A, B
369Human gammaherpesvirus 8Mutation(s): 2 
Gene Names: ORF74
Membrane Entity: Yes 
UniProt
Find proteins for Q98146 (Human herpesvirus 8 type P (isolate GK18))
Explore Q98146 
Go to UniProtKB:  Q98146
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98146
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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 StatesR01CA251275

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Data collection, Database references