4ADF Immune System Receptor date Dec 23, 2011
title Crystal Structure Of The Human Colony-Stimulating Factor 1 ( Cytokine In Complex With The Viral Receptor Barf1
authors J.Elegheert, N.Bracke, S.N.Savvides
compound source
Molecule: Secreted Protein Barf1
Chain: A, B, C, D, E, F, M, N, O, P, Q, R
Synonym: Barf1,33 Kda Early Protein, P33
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Herpesvirus 4
Organism_taxid: 10376
Strain: B95-8
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
Expression_system_vector_type: Plasmid
Expression_system_vector: Phlsec

Molecule: Macrophage Colony-Stimulating Factor 1
Chain: G, H, I, J, K, L, S, T, U, V, W, X
Fragment: Unp Residues 33-181
Synonym: Hcsf-1, Csf-1, M-Csf, Mcsf, Lanimostim, Processed Colony-Stimulating Factor 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codonplus Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet15b
symmetry Space Group: P 31 2 1
R_factor 0.238 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
218.440 218.440 331.170 90.00 90.00 120.00
method X-Ray Diffractionresolution 4.40 Å
ligand BMA, MAN, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, N, E, Q, M, C, A, O, P, B, D, R


S, T, K, V, L, J, W, X, H, I, G, U


Primary referenceAllosteric competitive inactivation of hematopoietic CSF-1 signaling by the viral decoy receptor BARF1., Elegheert J, Bracke N, Pouliot P, Gutsche I, Shkumatov AV, Tarbouriech N, Verstraete K, Bekaert A, Burmeister WP, Svergun DI, Lambrecht BN, Vergauwen B, Savvides SN, Nat Struct Mol Biol. 2012 Sep;19(9):938-47. doi: 10.1038/nsmb.2367. Epub 2012 Aug, 19. PMID:22902366
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (672 Kb) [Save to disk]
  • Biological Unit Coordinates (4adf.pdb1.gz) 334 Kb
  • Biological Unit Coordinates (4adf.pdb2.gz) 336 Kb
  • LPC: Ligand-Protein Contacts for 4ADF
  • CSU: Contacts of Structural Units for 4ADF
  • Structure Factors (1127 Kb)
  • Retrieve 4ADF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ADF from S2C, [Save to disk]
  • Re-refined 4adf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ADF 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 4ADF
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4ADF, from MSDmotif at EBI
  • Fold representative 4adf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4adf_J] [4adf_V] [4adf_G] [4adf_U] [4adf_M] [4adf_F] [4adf_R] [4adf_Q] [4adf_T] [4adf_H] [4adf_L] [4adf_N] [4adf_P] [4adf_C] [4adf] [4adf_I] [4adf_E] [4adf_O] [4adf_X] [4adf_K] [4adf_A] [4adf_D] [4adf_B] [4adf_S] [4adf_W]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4ADF: [IG_like ] by SMART
  • Other resources with information on 4ADF
  • Community annotation for 4ADF at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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