4ZLT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.5 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: 10.1016/j.str.2015.10.018
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: fremont@wustl.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
B, A
420Cricetid gammaherpesvirus 2Mutation(s): 4 
Find proteins for E9M5R0 (Cricetid gammaherpesvirus 2)
Go to UniProtKB:  E9M5R0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-C motif chemokine 3
F, L
70Mus musculusMutation(s): 1 
Gene Names: Ccl3 (Mip1a, Scya3)
Find proteins for P10855 (Mus musculus)
Go to UniProtKB:  P10855
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.493α = 90.00
b = 109.482β = 90.00
c = 210.956γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-30
    Type: Database references
  • Version 1.2: 2016-01-20
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence
  • Version 1.5: 2018-08-22
    Type: Data collection