4ZLT

Crystal structure of viral chemokine binding protein R17 in complex with CCL3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.8 of the entry. See complete history


Literature

Parallel Evolution of Chemokine Binding by Structurally Related Herpesvirus Decoy Receptors.

Lubman, O.Y.Fremont, D.H.

(2016) Structure 24: 57-69

  • DOI: https://doi.org/10.1016/j.str.2015.10.018
  • Primary Citation of Related Structures:  
    4ZKQ, 4ZLT

  • PubMed Abstract: 

    A wide variety of pathogens targets chemokine signaling networks in order to disrupt host immune surveillance and defense. Here, we report a structural and mutational analysis of rodent herpesvirus Peru encoded R17, a potent chemokine inhibitor that sequesters CC and C chemokines with high affinity. R17 consists of a pair of β-sandwich domains linked together by a bridging sheet, which form an acidic binding cleft for the chemokine CCL3 on the opposite face of a basic surface cluster that binds glycosaminoglycans. R17 promiscuously engages chemokines primarily through the same N-loop determinants used for host receptor recognition while residues located in the chemokine 40s loop drive kinetically stable complex formation. The core fold adopted by R17 is unexpectedly similar to that of the M3 chemokine decoy receptor encoded by MHV-68, although, strikingly, neither the location of ligand engagement nor the stoichiometry of binding is conserved, suggesting that their functions evolved independently.


  • Organizational Affiliation

    Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinA [auth B],
B [auth A]
420Cricetid gammaherpesvirus 2Mutation(s): 4 
Gene Names: RHVP-L.R17RHVP.R17
UniProt
Find proteins for E9M5R0 (Cricetid gammaherpesvirus 2)
Explore E9M5R0 
Go to UniProtKB:  E9M5R0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9M5R0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-C motif chemokine 3C [auth F],
D [auth L]
70Mus musculusMutation(s): 1 
Gene Names: Ccl3Mip1aScya3
UniProt & NIH Common Fund Data Resources
Find proteins for P10855 (Mus musculus)
Explore P10855 
Go to UniProtKB:  P10855
IMPC:  MGI:98260
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10855
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.493α = 90
b = 109.482β = 90
c = 210.956γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI019687
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54 AI057160
Center for Women Infectious Disease ResearchUnited States--
Washington University/Pfizer AgreementUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-30
    Changes: Database references
  • Version 1.2: 2016-01-20
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.5: 2018-08-22
    Changes: Data collection
  • Version 1.6: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.7: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.8: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary