Experimental Data Snapshot
(2012) Proc Natl Acad Sci U S A 109: 12962-12967
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.
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (NAG)
Biological assembly 1 assigned by authors and generated by PISA (software)
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (NAG)
Biological assembly 2 assigned by authors and generated by PISA (software)
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (NAG)
Biological assembly 3 assigned by authors and generated by PISA (software)
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (NAG)
Biological assembly 4 assigned by authors and generated by PISA (software)
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Secreted protein BARF1 | A, B, C [auth D] | 203 | human gammaherpesvirus 4 | Mutation(s): 0  Gene Names: BARF1 | ![]() |
UniProt | |||||
Find proteins for P0CW72 (Epstein-Barr virus (strain GD1)) Explore P0CW72  Go to UniProtKB:  P0CW72 | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0CW72 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | |||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Macrophage colony-stimulating factor 1 | D [auth E], E [auth F], F [auth G] | 147 | Homo sapiens | Mutation(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 Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P09603 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | Go to GlyGen: P09603-1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G [auth C], H, I | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE | |||||
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG Download Ideal Coordinates CCD File  | J [auth E], K [auth F], L [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 199.554 | α = 90 |
| b = 162.701 | β = 95.87 |
| c = 57.337 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
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.