7S59 | pdb_00007s59

Crystal structure of the tick evasin EVA-P974 complexed to a chimera made of human chemokines CCL7 and CCL8

• PDB DOI: https://doi.org/10.2210/pdb7S59/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Amblyomma cajennense, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-10 Released: 2022-03-16 
• Deposition Author(s): Bhusal, R.P., Devkota, S.R., Aryal, P., Wilce, M.C.J., Stone, M.J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.268 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Structure-guided engineering of tick evasins for targeting chemokines in inflammatory diseases.

Bhusal, R.P., Aryal, P., Devkota, S.R., Pokhrel, R., Gunzburg, M.J., Foster, S.R., Lim, H.D., Payne, R.J., Wilce, M.C.J., Stone, M.J.

(2022) Proc Natl Acad Sci U S A 119

• PubMed: 35217625 
• DOI: https://doi.org/10.1073/pnas.2122105119
• Primary Citation Related Structures: 
  7S4N, 7S58, 7S59, 7S5A, 7SO0


• PubMed Abstract: 
  

  As natural chemokine inhibitors, evasin proteins produced in tick saliva are potential therapeutic agents for numerous inflammatory diseases. Engineering evasins to block the desired chemokines and avoid off-target side effects requires structural understanding of their target selectivity. Structures of the class A evasin EVA-P974 bound to human CC chemokine ligands 7 and 17 (CCL7 and CCL17) and to a CCL8-CCL7 chimera reveal that the specificity of class A evasins for chemokines of the CC subfamily is defined by conserved, rigid backbone-backbone interactions, whereas the preference for a subset of CC chemokines is controlled by side-chain interactions at four hotspots in flexible structural elements. Hotspot mutations alter target preference, enabling inhibition of selected chemokines. The structure of an engineered EVA-P974 bound to CCL2 reveals an underlying molecular mechanism of EVA-P974 target preference. These results provide a structure-based framework for engineering evasins as targeted antiinflammatory therapeutics.

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Organizational Affiliation: 
• Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; [e-mail] [e-mail].
Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.41 kDa 
• Atom Count: 2,302 
• Modeled Residue Count: 306 
• Deposited Residue Count: 322 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Evasin P974	A [auth 1], B [auth 3]	85	Amblyomma cajennense	Mutation(s): 0
UniProt
Find proteins for A0A023FDY8 (Amblyomma cajennense) Explore A0A023FDY8  Go to UniProtKB:  A0A023FDY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7	C [auth 4], D [auth 2]	76	Homo sapiens	Mutation(s): 0  Gene Names: CCL8, MCP2, SCYA10, SCYA8, CCL7, MCP3, SCYA6, SCYA7
UniProt & NIH Common Fund Data Resources
Find proteins for P80075 (Homo sapiens) Explore P80075  Go to UniProtKB:  P80075
PHAROS:  P80075 GTEx:  ENSG00000108700
Find proteins for P80098 (Homo sapiens) Explore P80098  Go to UniProtKB:  P80098
PHAROS:  P80098 GTEx:  ENSG00000108688
UniProt Groups	P80075P80098

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	E [auth 1], F [auth 4]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.268 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.24	α = 90
b = 62.718	β = 93.933
c = 53.966	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Bhusal, R.P., Devkota, S.R., Aryal, P., Wilce, M.C.J., Stone, M.J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary