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 4FA8|pdb_00004fa8

Multi-pronged modulation of cytokine signaling


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.260 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Multipronged attenuation of macrophage-colony stimulating factor signaling by Epstein-Barr virus BARF1.

Shim, A.H.Chang, R.A.Chen, X.Longnecker, R.He, X.

(2012) Proc Natl Acad Sci U S A 109: 12962-12967

  • PubMed22826234 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1073/pnas.1205309109
  • Primary Citation of Related Structures:  
    4FA8

  • PubMed Abstract: 

    The ubiquitous EBV causes infectious mononucleosis and is associated with several types of cancers. The EBV genome encodes an early gene product, BARF1, which contributes to pathogenesis, potentially through growth-altering and immune-modulating activities, but the mechanisms for such activities are poorly understood. We have determined the crystal structure of BARF1 in complex with human macrophage-colony stimulating factor (M-CSF), a hematopoietic cytokine with pleiotropic functions in development and immune response. BARF1 and M-CSF form a high-affinity, stable, ring-like complex in both solution and the crystal, with a BARF1 hexameric ring surrounded by three M-CSF dimers in triangular array. The binding of BARF1 to M-CSF dramatically reduces but does not completely abolish M-CSF binding and signaling through its cognate receptor FMS. A three-pronged down-regulation mechanism is proposed to explain the biological effect of BARF1 on M-CSF:FMS signaling. These prongs entail control of the circulating and effective local M-CSF concentration, perturbation of the receptor-binding surface of M-CSF, and imposition of an unfavorable global orientation of the M-CSF dimer. Each prong may reduce M-CSF:FMS signaling to a limited extent but in combination may alter M-CSF:FMS signaling dramatically. The downregulating mechanism of BARF1 underlines a viral modulation strategy, and provides a basis for understanding EBV pathogenesis.


  • Organizational Affiliation
    • Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
Biological Assembly 1  

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Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 


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Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 


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Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (NAG)


Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 


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Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (NAG)


Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 


Find Similar Assemblies

Biological assembly 4 assigned by authors and generated by PISA (software)

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Macromolecule Content 

  • Total Structure Weight: 121.97 kDa 
  • Atom Count: 8,676 
  • Modeled Residue Count: 1,003 
  • Deposited Residue Count: 1,050 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Secreted protein BARF1A,
B,
C [auth D]
203human gammaherpesvirus 4Mutation(s): 0 
Gene Names: BARF1
UniProt
Find proteins for P0CW72 (Epstein-Barr virus (strain GD1))
Explore P0CW72 
Go to UniProtKB:  P0CW72
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CW72
Glycosylation
Glycosylation Sites: 1
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 1D [auth E],
E [auth F],
F [auth G]
147Homo sapiensMutation(s): 0 
Gene Names: CSF1
UniProt & NIH Common Fund Data Resources
Find proteins for P09603 (Homo sapiens)
Explore P09603 
Go to UniProtKB:  P09603
PHAROS:  P09603
GTEx:  ENSG00000184371 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09603
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P09603-1
Sequence Annotations
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  • 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-glucopyranoseG [auth C],
H,
I
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.260 (Depositor), 0.262 (DCC) 
  • R-Value Work: 0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.554α = 90
b = 162.701β = 95.87
c = 57.337γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Refinement description, Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.


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