4ADQ

CRYSTAL STRUCTURE OF THE MOUSE COLONY-STIMULATING FACTOR 1 (MCSF-1) CYTOKINE IN COMPLEX WITH THE VIRAL RECEPTOR BARF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Allosteric Competitive Inactivation of Hematopoietic Csf-1 Signaling by the Viral Decoy Receptor Barf1.

Elegheert, J.Bracke, N.Pouliot, P.Gutsche, I.Shkumatov, A.V.Tarbouriech, N.Verstraete, K.Bekaert, A.Burmeister, W.P.Svergun, D.I.Lambrecht, B.N.Vergauwen, B.Savvides, S.N.

(2012) Nat Struct Mol Biol 19: 938

  • DOI: https://doi.org/10.1038/nsmb.2367
  • Primary Citation of Related Structures:  
    3UEZ, 3UF2, 3UF5, 4ADF, 4ADQ

  • PubMed Abstract: 

    Hematopoietic human colony-stimulating factor 1 (hCSF-1) is essential for innate and adaptive immunity against viral and microbial infections and cancer. The human pathogen Epstein-Barr virus secretes the lytic-cycle protein BARF1 that neutralizes hCSF-1 to achieve immunomodulation. Here we show that BARF1 binds the dimer interface of hCSF-1 with picomolar affinity, away from the cognate receptor-binding site, to establish a long-lived complex featuring three hCSF-1 at the periphery of the BARF1 toroid. BARF1 locks dimeric hCSF-1 into an inactive conformation, rendering it unable to signal via its cognate receptor on human monocytes. This reveals a new functional role for hCSF-1 cooperativity in signaling. We propose a new viral strategy paradigm featuring an allosteric decoy receptor of the competitive type, which couples efficient sequestration and inactivation of the host growth factor to abrogate cooperative assembly of the cognate signaling complex.


  • Organizational Affiliation

    Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry & Microbiology, Ghent University, Ghent, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SECRETED PROTEIN BARF1
A, B, C, D
208human gammaherpesvirus 4Mutation(s): 1 
UniProt
Find proteins for P03228 (Epstein-Barr virus (strain B95-8))
Explore P03228 
Go to UniProtKB:  P03228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03228
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MACROPHAGE COLONY-STIMULATING FACTOR 1
E, F, G, H
153Mus musculusMutation(s): 0 
UniProt
Find proteins for P07141 (Mus musculus)
Explore P07141 
Go to UniProtKB:  P07141
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07141
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, K, L
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 234.75α = 90
b = 234.75β = 90
c = 96.04γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 1.2: 2018-02-28
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary