3ONA

The SECRET domain in complex with CX3CL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1371/journal.ppat.1002162
  • Primary Citation of Related Structures:  
    3ON9, 3ONA

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumour necrosis factor receptor163Ectromelia virusMutation(s): 0 
Gene Names: crmD
UniProt
Find proteins for Q7TDW8 (Ectromelia virus)
Explore Q7TDW8 
Go to UniProtKB:  Q7TDW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7TDW8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CX3CL1 protein80Homo sapiensMutation(s): 0 
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
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.33α = 90
b = 71.33β = 90
c = 93.141γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary