PDBsum entry 2e9w

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protein ligands Protein-protein interface(s) links
Transferase/hormone PDB id
Protein chains
468 a.a. *
132 a.a. *
NAG ×6
* Residue conservation analysis
PDB id:
Name: Transferase/hormone
Title: Crystal structure of the extracellular domain of kit in comp stem cell factor (scf)
Structure: Mast/stem cell growth factor receptor. Chain: a, b. Fragment: extracellular domains, d1 - d5. Synonym: scfr, proto-oncogene tyrosine-protein kinase kit, cd117 antigen. Engineered: yes. Mutation: yes. Kit ligand. Chain: c, d.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: kit. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Gene: scf. Expressed in: escherichia coli.
3.50Å     R-factor:   0.245     R-free:   0.294
Authors: S.Yuzawa,Y.Opatowsky,Z.Zhang,V.Mandiyan,I.Lax,J.Schlessinger
Key ref:
S.Yuzawa et al. (2007). Structural basis for activation of the receptor tyrosine kinase KIT by stem cell factor. Cell, 130, 323-334. PubMed id: 17662946 DOI: 10.1016/j.cell.2007.05.055
27-Jan-07     Release date:   07-Aug-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P10721  (KIT_HUMAN) -  Mast/stem cell growth factor receptor Kit
976 a.a.
468 a.a.*
Protein chains
Pfam   ArchSchema ?
P21583  (SCF_HUMAN) -  Kit ligand
273 a.a.
132 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Receptor protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Bound ligand (Het Group name = NAG)
matches with 47.62% similarity
+ [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     membrane   1 term 
  Biological process     cell adhesion   1 term 
  Biochemical function     stem cell factor receptor binding     1 term  


DOI no: 10.1016/j.cell.2007.05.055 Cell 130:323-334 (2007)
PubMed id: 17662946  
Structural basis for activation of the receptor tyrosine kinase KIT by stem cell factor.
S.Yuzawa, Y.Opatowsky, Z.Zhang, V.Mandiyan, I.Lax, J.Schlessinger.
Stem Cell Factor (SCF) initiates its multiple cellular responses by binding to the ectodomain of KIT, resulting in tyrosine kinase activation. We describe the crystal structure of the entire ectodomain of KIT before and after SCF stimulation. The structures show that KIT dimerization is driven by SCF binding whose sole role is to bring two KIT molecules together. Receptor dimerization is followed by conformational changes that enable lateral interactions between membrane proximal Ig-like domains D4 and D5 of two KIT molecules. Experiments with cultured cells show that KIT activation is compromised by point mutations in amino acids critical for D4-D4 interaction. Moreover, a variety of oncogenic mutations are mapped to the D5-D5 interface. Since key hallmarks of KIT structures, ligand-induced receptor dimerization, and the critical residues in the D4-D4 interface, are conserved in other receptors, the mechanism of KIT stimulation unveiled in this report may apply for other receptor activation.
  Selected figure(s)  
Figure 2.
Figure 2. Crystal Structure of the SCF-KIT Ectodomain 2:2 Complex
(A) Ribbon diagram of the SCF-KIT 2:2 complex. Color coding of D1 to D5 is the same as in Figure 1 and SCF is colored in magenta. N and C termini of KIT and SCF are labeled. Disulfide bonds in D1 and D5 are shown in ball-and-stick rendering with sulfur atoms colored in orange. Asparagine-linked carbohydrates are represented in a stick model. Arrow marks a large cavity in the SCF-KIT 2:2 complex. (See stereo view in Figure S2.)
(B) Surface representations of the SCF-KIT ectodomain 2:2 complex. The figures show a top view (top), face view (center left), side view (center right), and bottom view (low). Color coding is the same as in (A). The views show that a SCF dimer interacts symmetrically with D1, D2, and D3 of two corresponding KIT ectodomains. In addition, KIT ectodomains form homophylic interactions through lateral contacts between D4 (orange) and between D5 (pink) of two neighboring receptors.
Figure 6.
Figure 6. Views of the D4-D4 and D5-D5 Interfaces
(A) 2Fo-Fc electron density map contoured at 1.1σ level showing a view of the D4-D4 interface (top panel). The backbones of KIT protomers are represented as pink and yellow tubes, respectively. A close view (bottom panel) of the D4-D4 interface of two neighboring ectodomains is shown. Interchain hydrogren bonds formed between Arg381 and Glu386 of two adjacent D4 are colored in yellow. Key amino acids are labeled and shown as a stick model. Secondary structure elements are labeled according to the IgSF nomenclature.
(B) Conservation of the D4-D4 dimerization motif across members of type III and type V RTK families. Residues 370–398 of human KIT (AAC50969.1) aligned with sequences of (with accession numbers) mouse (AAH75716.1), chicken (NP_989692.1), Xenopus laevis (AAH61947), salamander (AAS91161.1), and zebrafish (type A and B (NP_571128, XP_691901) homologs. Also shown are amino-acid sequences of CSF1R from human (P07333), mouse (P09581), and torafugu type A and B (P79750, Q8UVR8) and sequences from PDGFRα and PDGFRβ from human (P16234, P09619) and mouse (NP_035188, P05622). Amino-acid sequences of type V RTKs of human VEGFR type 1–3 (7^th Ig-like domain) (P17948, P35968, and P35916) are also presented. Secondary structure elements on KIT are labeled on the top of the sequence alignment. The conserved residues of Arg381 and Lys383, Leu382 and Leu379, and Glu386 and Gly388 are colored in blue, yellow, red, and green, respectively.
(C) Ribbon diagram of a D5-D5 interface. Strands A and G of two adjacent KIT protomers participate in formation of the D5-D5 interface. The D5-D5 interface is maintained by lateral interactions between Tyr418 and Asn505 of two neighboring receptors probably through ion(s) or water molecule(s).
(D) Electrostatic potential surfaces of D4 and D5 of KIT. The figures show a face view of the D4-D4 interacting surface (right) and a view following 90° rotation along the vertical axis (left). The position of acidic patch and the D4-D4 interfaces are circled and the interacting residue Arg381 and Glu386 are labeled.
  The above figures are reprinted by permission from Cell Press: Cell (2007, 130, 323-334) copyright 2007.  
  Figures were selected by an automated process.  

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.  
22089421 C.L.Corless, C.M.Barnett, and M.C.Heinrich (2011).
Gastrointestinal stromal tumours: origin and molecular oncology.
  Nat Rev Cancer, 11, 865-878.  
21125679 C.R.Antonescu (2011).
The GIST paradigm: lessons for other kinase-driven cancers.
  J Pathol, 223, 251-261.  
21397181 G.T.Johnson, L.Autin, D.S.Goodsell, M.F.Sanner, and A.J.Olson (2011).
ePMV embeds molecular modeling into professional animation software environments.
  Structure, 19, 293-303.  
21383156 Z.J.Ye, E.Gulcicek, K.Stone, T.Lam, V.Schulz, and S.M.Weissman (2011).
Complex interactions in EML cell stimulation by stem cell factor and IL-3.
  Proc Natl Acad Sci U S A, 108, 4882-4887.  
20534510 A.H.Shim, H.Liu, P.J.Focia, X.Chen, P.C.Lin, and X.He (2010).
Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex.
  Proc Natl Acad Sci U S A, 107, 11307-11312.
PDB codes: 3mjg 3mjk
19865100 C.Bodemer, O.Hermine, F.Palmérini, Y.Yang, C.Grandpeix-Guyodo, P.S.Leventhal, S.Hadj-Rabia, L.Nasca, S.Georgin-Lavialle, A.Cohen-Akenine, J.M.Launay, S.Barete, F.Feger, M.Arock, B.Catteau, B.Sans, J.F.Stalder, F.Skowron, L.Thomas, G.Lorette, P.Plantin, P.Bordigoni, O.Lortholary, Prost, A.Moussy, H.Sobol, and P.Dubreuil (2010).
Pediatric mastocytosis is a clonal disease associated with D816V and other activating c-KIT mutations.
  J Invest Dermatol, 130, 804-815.  
20581310 F.Toffalini, and J.B.Demoulin (2010).
New insights into the mechanisms of hematopoietic cell transformation by activated receptor tyrosine kinases.
  Blood, 116, 2429-2437.  
20838788 G.J.Molderings, K.Meis, U.W.Kolck, J.Homann, and T.Frieling (2010).
Comparative analysis of mutation of tyrosine kinase kit in mast cells from patients with systemic mast cell activation syndrome and healthy subjects.
  Immunogenetics, 62, 721-727.  
20432069 J.H.Bae, and J.Schlessinger (2010).
Asymmetric tyrosine kinase arrangements in activation or autophosphorylation of receptor tyrosine kinases.
  Mol Cells, 29, 443-448.  
20361266 P.A.Cassier, and J.Y.Blay (2010).
Molecular response prediction in gastrointestinal stromal tumors.
  Target Oncol, 5, 29-37.  
20145116 V.M.Leppänen, A.E.Prota, M.Jeltsch, A.Anisimov, N.Kalkkinen, T.Strandin, H.Lankinen, A.Goldman, K.Ballmer-Hofer, and K.Alitalo (2010).
Structural determinants of growth factor binding and specificity by VEGF receptor 2.
  Proc Natl Acad Sci U S A, 107, 2425-2430.
PDB codes: 2x1w 2x1x
20080685 Y.Yang, P.Xie, Y.Opatowsky, and J.Schlessinger (2010).
Direct contacts between extracellular membrane-proximal domains are required for VEGF receptor activation and cell signaling.
  Proc Natl Acad Sci U S A, 107, 1906-1911.
PDB code: 3kvq
20484085 Y.Yang, S.Létard, L.Borge, A.Chaix, K.Hanssens, S.Lopez, M.Vita, P.Finetti, D.Birnbaum, F.Bertucci, S.Gomez, Sepulveda, and P.Dubreuil (2010).
Pediatric mastocytosis-associated KIT extracellular domain mutations exhibit different functional and signaling properties compared with KIT-phosphotransferase domain mutations.
  Blood, 116, 1114-1123.  
20595514 Z.Orinska, N.Föger, M.Huber, J.Marschall, F.Mirghomizadeh, X.Du, M.Scheller, P.Rosenstiel, T.Goldmann, A.Bollinger, B.A.Beutler, and S.Bulfone-Paus (2010).
I787 provides signals for c-Kit receptor internalization and functionality that control mast cell survival and development.
  Blood, 116, 2665-2675.  
19637142 D.Margulies, Y.Opatowsky, S.Fletcher, I.Saraogi, L.K.Tsou, S.Saha, I.Lax, J.Schlessinger, and A.D.Hamilton (2009).
Surface binding inhibitors of the SCF-KIT protein-protein interaction.
  Chembiochem, 10, 1955-1958.  
19658168 E.Stuttfeld, and K.Ballmer-Hofer (2009).
Structure and function of VEGF receptors.
  IUBMB Life, 61, 915-922.  
19135393 P.Tolar, J.Hanna, P.D.Krueger, and S.K.Pierce (2009).
The constant region of the membrane immunoglobulin mediates B cell-receptor clustering and signaling in response to membrane antigens.
  Immunity, 30, 44-55.  
19861442 T.Guo, M.Hajdu, N.P.Agaram, H.Shinoda, D.Veach, B.D.Clarkson, R.G.Maki, S.Singer, R.P.Dematteo, P.Besmer, and C.R.Antonescu (2009).
Mechanisms of sunitinib resistance in gastrointestinal stromal tumors harboring KITAY502-3ins mutation: an in vitro mutagenesis screen for drug resistance.
  Clin Cancer Res, 15, 6862-6870.  
18697750 J.Sun, M.Pedersen, and L.Rönnstrand (2008).
Gab2 Is Involved in Differential Phosphoinositide 3-Kinase Signaling by Two Splice Forms of c-Kit.
  J Biol Chem, 283, 27444-27451.  
18573086 K.M.Ferguson (2008).
Structure-based view of epidermal growth factor receptor regulation.
  Annu Rev Biophys, 37, 353-373.  
18955458 M.C.Heinrich, R.G.Maki, C.L.Corless, C.R.Antonescu, A.Harlow, D.Griffith, A.Town, A.McKinley, W.B.Ou, J.A.Fletcher, C.D.Fletcher, X.Huang, D.P.Cohen, C.M.Baum, and G.D.Demetri (2008).
Primary and secondary kinase genotypes correlate with the biological and clinical activity of sunitinib in imatinib-resistant gastrointestinal stromal tumor.
  J Clin Oncol, 26, 5352-5359.  
18640841 P.De Meyts (2008).
The insulin receptor: a prototype for dimeric, allosteric membrane receptors?
  Trends Biochem Sci, 33, 376-384.  
19017797 X.Chen, H.Liu, P.J.Focia, A.H.Shim, and X.He (2008).
Structure of macrophage colony stimulating factor bound to FMS: diverse signaling assemblies of class III receptor tyrosine kinases.
  Proc Natl Acad Sci U S A, 105, 18267-18272.
PDB code: 3ejj
18505839 Y.Yang, S.Yuzawa, and J.Schlessinger (2008).
Contacts between membrane proximal regions of the PDGF receptor ectodomain are required for receptor activation but not for receptor dimerization.
  Proc Natl Acad Sci U S A, 105, 7681-7686.  
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.