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PDBsum entry 4dkd

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protein ligands Protein-protein interface(s) links
Cytokine/transferase PDB id
4dkd
Jmol
Contents
Protein chains
161 a.a.
272 a.a.
Ligands
NAG-NAG ×2
BMA ×2
NAG ×4
Waters ×16
PDB id:
4dkd
Name: Cytokine/transferase
Title: Crystal structure of human interleukin-34 bound to human csf
Structure: Interleukin-34. Chain: a, b. Fragment: active core, unp residues 21-193. Synonym: il-34. Engineered: yes. Macrophage colony-stimulating factor 1 receptor. Chain: c. Fragment: d1-d3, unp residues 20-299. Synonym: csf-1 receptor, csf-1-r, csf-1r, m-csf-r, proto-on
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: il34, c16orf77. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: tni pro. Gene: csf1r, fms. Expression_system_cell_line: tni pro
Resolution:
3.00Å     R-factor:   0.254     R-free:   0.287
Authors: X.Ma,J.F.Bazan,M.A.Starovasnik
Key ref: X.Ma et al. (2012). Structural basis for the dual recognition of helical cytokines IL-34 and CSF-1 by CSF-1R. Structure, 20, 676-687. PubMed id: 22483114 DOI: 10.1016/j.str.2012.02.010
Date:
03-Feb-12     Release date:   11-Apr-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q6ZMJ4  (IL34_HUMAN) -  Interleukin-34
Seq:
Struc:
242 a.a.
161 a.a.
Protein chain
Pfam   ArchSchema ?
P07333  (CSF1R_HUMAN) -  Macrophage colony-stimulating factor 1 receptor
Seq:
Struc:
 
Seq:
Struc:
972 a.a.
272 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain C: E.C.2.7.10.1  - Receptor protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP
+
[protein]-L-tyrosine
Bound ligand (Het Group name = NAG)
matches with 47.62% similarity
= ADP
+ [protein]-L-tyrosine phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   1 term 
  Biological process     positive regulation of cell proliferation   2 terms 
  Biochemical function     macrophage colony-stimulating factor receptor binding     1 term  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2012.02.010 Structure 20:676-687 (2012)
PubMed id: 22483114  
 
 
Structural basis for the dual recognition of helical cytokines IL-34 and CSF-1 by CSF-1R.
X.Ma, W.Y.Lin, Y.Chen, S.Stawicki, K.Mukhyala, Y.Wu, F.Martin, J.F.Bazan, M.A.Starovasnik.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22902366 J.Elegheert, N.Bracke, P.Pouliot, I.Gutsche, A.V.Shkumatov, N.Tarbouriech, K.Verstraete, A.Bekaert, W.P.Burmeister, D.I.Svergun, B.N.Lambrecht, B.Vergauwen, and S.N.Savvides (2012).
Allosteric competitive inactivation of hematopoietic CSF-1 signaling by the viral decoy receptor BARF1.
  Nat Struct Mol Biol, 19, 938-947.
PDB codes: 3uez 3uf2 3uf5 4adf 4adq
23076159 K.Verstraete, and S.N.Savvides (2012).
Extracellular assembly and activation principles of oncogenic class III receptor tyrosine kinases.
  Nat Rev Cancer, 12, 753-766.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.