6I31

Crystal structure of the tick chemokine-binding protein Evasin-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A knottin scaffold directs the CXC-chemokine-binding specificity of tick evasins.

Lee, A.W.Deruaz, M.Lynch, C.Davies, G.Singh, K.Alenazi, Y.Eaton, J.R.O.Kawamura, A.Shaw, J.Proudfoot, A.E.I.Dias, J.M.Bhattacharya, S.

(2019) J Biol Chem 294: 11199-11212

  • DOI: https://doi.org/10.1074/jbc.RA119.008817
  • Primary Citation of Related Structures:  
    6I31

  • PubMed Abstract: 

    Tick evasins (EVAs) bind either CC- or CXC-chemokines by a poorly understood promiscuous or "one-to-many" mechanism to neutralize inflammation. Because EVAs potently inhibit inflammation in many preclinical models, highlighting their potential as biological therapeutics for inflammatory diseases, we sought to further unravel the CXC-chemokine-EVA interactions. Using yeast surface display, we identified and characterized 27 novel CXC-chemokine-binding evasins homologous to EVA3 and defined two functional classes. The first, which included EVA3, exclusively bound ELR + CXC-chemokines, whereas the second class bound both ELR + and ELR - CXC-chemokines, in several cases including C X C-motif chemokine ligand 10 (CXCL10) but, surprisingly, not CXCL8. The X-ray crystal structure of EVA3 at a resolution of 1.79 Å revealed a single antiparallel β-sheet with six conserved cysteine residues forming a disulfide-bonded knottin scaffold that creates a contiguous solvent-accessible surface. Swapping analyses identified distinct knottin scaffold segments necessary for different CXC-chemokine-binding activities, implying that differential ligand positioning, at least in part, plays a role in promiscuous binding. Swapping segments also transferred chemokine-binding activity, resulting in a hybrid EVA with dual CXCL10- and CXCL8-binding activities. The solvent-accessible surfaces of the knottin scaffold segments have distinctive shape and charge, which we suggest drives chemokine-binding specificity. These studies provide structural and mechanistic insight into how CXC-chemokine-binding tick EVAs achieve class specificity but also engage in promiscuous binding.


  • Organizational Affiliation

    Radcliffe Department of Medicine Division of Cardiovascular Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Evasin-3
A, B
66Rhipicephalus sanguineusMutation(s): 0 
UniProt
Find proteins for P0C8E8 (Rhipicephalus sanguineus)
Explore P0C8E8 
Go to UniProtKB:  P0C8E8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C8E8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.09α = 90
b = 55.09β = 90
c = 71.04γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
British Heart FoundationUnited KingdomPG/16/100/32632

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references