8XWN | pdb_00008xwn

Structure of CXCR2 bound to CXCL8 (Ligand-receptor focused map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of promiscuous chemokine binding and structural mimicry at the C-X-C chemokine receptor, CXCR2.

Saha, S.Sano, F.K.Sharma, S.Ganguly, M.Mishra, S.Dalal, A.Akasaka, H.Kobayashi, T.A.Zaidi, N.Tiwari, D.Roy, N.Yadav, M.K.Banerjee, N.Saha, S.Mohapatra, S.Itoh, Y.Chevigne, A.Banerjee, R.Shihoya, W.Nureki, O.Shukla, A.K.

(2025) Mol Cell 85: 976-988.e9

  • DOI: https://doi.org/10.1016/j.molcel.2025.01.024
  • Primary Citation of Related Structures:  
    8XVU, 8XWA, 8XWF, 8XWM, 8XWN, 8XWS, 8XWV, 8XX3, 8XX6, 8XX7, 8XXH, 8XXR, 8XXX

  • PubMed Abstract: 

    Selectivity of natural agonists for their cognate receptors is a hallmark of G-protein-coupled receptors (GPCRs); however, this selectivity often breaks down at the chemokine receptors. Chemokines often display promiscuous binding to chemokine receptors, but the underlying molecular determinants remain mostly elusive. Here, we perform a comprehensive transducer-coupling analysis, testing all known C-X-C chemokines on every C-X-C type chemokine receptor to generate a global fingerprint of the selectivity and promiscuity encoded within this system. Taking lead from this, we determine cryoelectron microscopy (cryo-EM) structures of the most promiscuous receptor, C-X-C chemokine receptor 2 (CXCR2), in complex with several chemokines. These structural snapshots elucidate the details of ligand-receptor interactions, including structural motifs, which are validated using mutagenesis and functional experiments. We also observe that most chemokines position themselves on CXCR2 as a dimer while CXCL6 exhibits a monomeric binding pose. Taken together, our findings provide the molecular basis of chemokine promiscuity at CXCR2 with potential implications for developing therapeutic molecules.


  • Organizational Affiliation
    • Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-X-C chemokine receptor type 2A [auth R]416Homo sapiensMutation(s): 0 
Gene Names: CXCR2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P25025 (Homo sapiens)
Explore P25025 
Go to UniProtKB:  P25025
PHAROS:  P25025
GTEx:  ENSG00000180871 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25025
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MDNCF-aB [auth D],
C [auth E]
79Homo sapiensMutation(s): 0 
Gene Names: CXCL8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P10145 (Homo sapiens)
Explore P10145 
Go to UniProtKB:  P10145
PHAROS:  P10145
GTEx:  ENSG00000169429 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10145
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.4
RECONSTRUCTIONRELION4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaIPA/2020/000405

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references