4FA8 Viral Protein Cytokine date May 21, 2012
title Multi-Pronged Modulation Of Cytokine Signaling
authors X.He, A.H.Shim
compound source
Molecule: Secreted Protein Barf1
Chain: A, B, D
Synonym: 33 Kda Early Protein, P33
Engineered: Yes
Organism_scientific: Human Herpesvirus 4
Organism_common: Hhv-4
Organism_taxid: 10376
Gene: Barf1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_organ: Human Embryonic Kidney Cells

Molecule: Macrophage Colony-Stimulating Factor 1
Chain: E, F, G
Fragment: Unp Residues 36-180
Synonym: Csf-1, M-Csf, Mcsf, Lanimostim, Processed Macropha Stimulating Factor 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Csf1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_organ: Human Embryonic Kidney Cells
symmetry Space Group: C 1 2 1
R_factor 0.222 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
199.554 162.701 57.337 90.00 95.87 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand BMA, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, G, E


Primary referenceMultipronged attenuation of macrophage-colony stimulating factor signaling by Epstein-Barr virus BARF1., Shim AH, Chang RA, Chen X, Longnecker R, He X, Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):12962-7. Epub 2012 Jul 23. PMID:22826234
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (359 Kb) [Save to disk]
  • Biological Unit Coordinates (4fa8.pdb1.gz) 697 Kb
  • Biological Unit Coordinates (4fa8.pdb2.gz) 392 Kb
  • Biological Unit Coordinates (4fa8.pdb3.gz) 105 Kb
  • Biological Unit Coordinates (4fa8.pdb4.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 4FA8
  • CSU: Contacts of Structural Units for 4FA8
  • Structure Factors (735 Kb)
  • Retrieve 4FA8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4FA8 from S2C, [Save to disk]
  • Re-refined 4fa8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4FA8 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4FA8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4FA8, from MSDmotif at EBI
  • Fold representative 4fa8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4fa8_D] [4fa8_A] [4fa8_B] [4fa8_F] [4fa8_G] [4fa8_E] [4fa8]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4FA8: [IG_like ] by SMART
  • Other resources with information on 4FA8
  • Community annotation for 4FA8 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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