3ONA

The SECRET domain in complex with CX3CL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of chemokine sequestration by CrmD, a poxvirus-encoded tumor necrosis factor receptor

Xue, X.G.Lu, Q.Y.Wei, H.Wang, D.L.Chen, D.W.He, G.J.Huang, L.Wang, H.Z.Wang, X.Q.

(2011) Plos Pathog. 7: e1002162-e1002162

  • DOI: 10.1371/journal.ppat.1002162
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pathogens have evolved sophisticated mechanisms to evade detection and destruction by the host immune system. Large DNA viruses encode homologues of chemokines and their receptors, as well as chemokine-binding proteins (CKBPs) to modulate the chemoki ...

    Pathogens have evolved sophisticated mechanisms to evade detection and destruction by the host immune system. Large DNA viruses encode homologues of chemokines and their receptors, as well as chemokine-binding proteins (CKBPs) to modulate the chemokine network in host response. The SECRET domain (smallpox virus-encoded chemokine receptor) represents a new family of viral CKBPs that binds a subset of chemokines from different classes to inhibit their activities, either independently or fused with viral tumor necrosis factor receptors (vTNFRs). Here we present the crystal structures of the SECRET domain of vTNFR CrmD encoded by ectromelia virus and its complex with chemokine CX3CL1. The SECRET domain adopts a β-sandwich fold and utilizes its β-sheet I surface to interact with CX3CL1, representing a new chemokine-binding manner of viral CKBPs. Structure-based mutagenesis and biochemical analysis identified important basic residues in the 40s loop of CX3CL1 for the interaction. Mutation of corresponding acidic residues in the SECRET domain also affected the binding for other chemokines, indicating that the SECRET domain binds different chemokines in a similar manner. We further showed that heparin inhibited the binding of CX3CL1 by the SECRET domain and the SECRET domain inhibited RAW264.7 cell migration induced by CX3CL1. These results together shed light on the structural basis for the SECRET domain to inhibit chemokine activities by interfering with both chemokine-GAG and chemokine-receptor interactions.


    Organizational Affiliation

    Center for Structural Biology, School of Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumour necrosis factor receptor
A
163Ectromelia virusMutation(s): 0 
Gene Names: crmD
Find proteins for Q7TDW8 (Ectromelia virus)
Go to UniProtKB:  Q7TDW8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CX3CL1 protein
B
80Homo sapiensMutation(s): 0 
Gene Names: CX3CL1 (FKN, NTT, SCYD1)
Find proteins for P78423 (Homo sapiens)
Go to Gene View: CX3CL1
Go to UniProtKB:  P78423
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.330α = 90.00
b = 71.330β = 90.00
c = 93.141γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references