4XT3

Structure of a viral GPCR bound to human chemokine CX3CL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.288 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor.

Burg, J.S.Ingram, J.R.Venkatakrishnan, A.J.Jude, K.M.Dukkipati, A.Feinberg, E.N.Angelini, A.Waghray, D.Dror, R.O.Ploegh, H.L.Garcia, K.C.

(2015) Science 347: 1113-1117

  • DOI: https://doi.org/10.1126/science.aaa5026
  • Primary Citation of Related Structures:  
    4XT1, 4XT3

  • PubMed Abstract: 

    Chemokines are small proteins that function as immune modulators through activation of chemokine G protein-coupled receptors (GPCRs). Several viruses also encode chemokines and chemokine receptors to subvert the host immune response. How protein ligands activate GPCRs remains unknown. We report the crystal structure at 2.9 angstrom resolution of the human cytomegalovirus GPCR US28 in complex with the chemokine domain of human CX3CL1 (fractalkine). The globular body of CX3CL1 is perched on top of the US28 extracellular vestibule, whereas its amino terminus projects into the central core of US28. The transmembrane helices of US28 adopt an active-state-like conformation. Atomic-level simulations suggest that the agonist-independent activity of US28 may be due to an amino acid network evolved in the viral GPCR to destabilize the receptor's inactive state.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor homolog US28362CytomegalovirusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P69332 (Human cytomegalovirus (strain AD169))
Explore P69332 
Go to UniProtKB:  P69332
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69332
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fractalkine91Homo sapiensMutation(s): 0 
Gene Names: CX3CL1FKNNTTSCYD1A-152E5.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P78423 (Homo sapiens)
Explore P78423 
Go to UniProtKB:  P78423
PHAROS:  P78423
GTEx:  ENSG00000006210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78423
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P78423-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
B
L-PEPTIDE LINKINGC5 H7 N O3GLN
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.288 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.9α = 90
b = 192.7β = 90
c = 94.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary