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PDBsum entry 2ec8
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References listed in PDB file
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Key reference
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Title
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Structural basis for activation of the receptor tyrosine kinase kit by stem cell factor.
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Authors
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S.Yuzawa,
Y.Opatowsky,
Z.Zhang,
V.Mandiyan,
I.Lax,
J.Schlessinger.
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Ref.
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Cell, 2007,
130,
323-334.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2007,
130,
323-334)
copyright 2007.
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