Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 104226.04 
• Atom Count: 6718 
• Residue Count: 950 
• Unique protein chains: 2

2NYZ

Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1

• DOI: 10.2210/pdb2NYZ/pdb

• Classification: VIRAL PROTEIN/CYTOKINE
• Organism(s): Homo sapiens, Murid herpesvirus 4
• Expression System: Spodoptera frugiperda


• Deposited: 2006-11-21 Released: 2007-12-25 
• Deposition Author(s): Alexander-Brett, J.M., Fremont, D.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.272 
• R-Value Work: 0.219 

Literature

Dual GPCR and GAG mimicry by the M3 chemokine decoy receptor.

Alexander-Brett, J.M., Fremont, D.H.

(2007) J.Exp.Med. 204: 3157-3172

• PubMed: 18070938 
• DOI: 10.1084/jem.20071677
• Primary Citation of Related Structures:  
  2NZ1


• PubMed Abstract: 
  

Viruses have evolved a myriad of evasion strategies focused on undermining chemokine-mediated immune surveillance, exemplified by the mouse gamma-herpesvirus 68 M3 decoy receptor. Crystal structures of M3 in complex with C chemokine ligand 1/lymphotactin and CC chemokine ligand 2/monocyte chemoattractant protein 1 reveal that invariant chemokine features associated with G protein-coupled receptor binding are primarily recognized by the decoy C-terminal domain, whereas the N-terminal domain (NTD) reconfigures to engage divergent basic residue clusters on the surface of chemokines. Favorable electrostatic forces dramatically enhance the association kinetics of chemokine binding by M3, with a primary role ascribed to acidic NTD regions that effectively mimic glycosaminoglycan interactions. Thus, M3 employs two distinct mechanisms of chemical imitation to potently sequester chemokines, thereby inhibiting chemokine receptor binding events as well as the formation of chemotactic gradients necessary for directed leukocyte trafficking.

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Organizational Affiliation: 

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hypothetical protein GAMMAHV.M3	A, B	382	Murid herpesvirus 4	Mutation(s): 0  Gene Names: GAMMAHV.M3 (M3)
Find proteins for O41925 (Murid herpesvirus 4) Go to UniProtKB:  O41925

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Lymphotactin	D, E	93	Homo sapiens	Mutation(s): 0  Gene Names: XCL1 (LTN, SCYC1)
Find proteins for P47992 (Homo sapiens) Go to Gene View: XCL1 Go to UniProtKB:  P47992

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.272 
• R-Value Work: 0.219 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 84.370	α = 90.00
b = 103.190	β = 90.00
c = 290.940	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-21 
• Released Date: 2007-12-25 
• Deposition Author(s): Alexander-Brett, J.M., Fremont, D.H.

Revision History 

• Version 1.0: 2007-12-25
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance