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- PDB-2e9w: Crystal structure of the extracellular domain of Kit in complex w... -

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Basic information

Entry
Database: PDB / ID: 2e9w
TitleCrystal structure of the extracellular domain of Kit in complex with stem cell factor (SCF)
Components
  • Kit ligandStem cell factor
  • Mast/stem cell growth factor receptor
KeywordsTRANSFERASE/HORMONE / Glycoprotein / Receptor tyrosine kinase / Growth factor cytokine / Dimerization / TRANSFERASE-HORMONE COMPLEX
Function / homology
Function and homology information


positive regulation of myeloid leukocyte differentiation / negative regulation of mast cell apoptotic process / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of hematopoietic stem cell proliferation / Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants ...positive regulation of myeloid leukocyte differentiation / negative regulation of mast cell apoptotic process / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of hematopoietic stem cell proliferation / Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants / Signaling by extracellular domain mutants of KIT / stem cell factor receptor activity / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / erythropoietin-mediated signaling pathway / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / positive regulation of dendritic cell cytokine production / Kit signaling pathway / positive regulation of melanocyte differentiation / regulation of bile acid metabolic process / positive regulation of small intestine smooth muscle contraction / mast cell apoptotic process / mast cell differentiation / positive regulation of mast cell proliferation / mast cell chemotaxis / myeloid leukocyte differentiation / Fc receptor signaling pathway / mast cell proliferation / positive regulation of long-term neuronal synaptic plasticity / glycosphingolipid metabolic process / detection of mechanical stimulus involved in sensory perception of sound / positive regulation of pseudopodium assembly / positive regulation of mast cell cytokine production / immature B cell differentiation / melanocyte differentiation / germ cell migration / lymphoid progenitor cell differentiation / myeloid progenitor cell differentiation / digestive tract development / positive regulation of Ras protein signal transduction / negative regulation of programmed cell death / neural crest cell migration / embryonic hemopoiesis / pigmentation / lamellipodium assembly / positive regulation of leukocyte migration / tongue development / megakaryocyte development / Regulation of KIT signaling / mast cell degranulation / stem cell population maintenance / cytokine binding / positive regulation of Notch signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / spermatid development / growth factor binding / somatic stem cell population maintenance / hemopoiesis / T cell differentiation / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / response to cadmium ion / positive regulation of phospholipase C activity / T cell proliferation / ovarian follicle development / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of T cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SH2 domain binding / transmembrane receptor protein tyrosine kinase activity / cell chemotaxis / erythrocyte differentiation / B cell differentiation / acrosomal vesicle / filopodium / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / epithelial cell proliferation / cytokine activity / stem cell differentiation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / visual learning / cytoplasmic side of plasma membrane / Signaling by SCF-KIT / response to organic cyclic compound / receptor protein-tyrosine kinase / fibrillar center / cytokine-mediated signaling pathway / male gonad development
Similarity search - Function
Stem cell factor / Stem cell factor / Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain ...Stem cell factor / Stem cell factor / Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Mast/stem cell growth factor receptor Kit / Kit ligand
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsYuzawa, S. / Opatowsky, Y. / Zhang, Z. / Mandiyan, V. / Lax, I. / Schlessinger, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structural Basis for Activation of the Receptor Tyrosine Kinase KIT by Stem Cell Factor
Authors: Yuzawa, S. / Opatowsky, Y. / Zhang, Z. / Mandiyan, V. / Lax, I. / Schlessinger, J.
History
DepositionJan 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mast/stem cell growth factor receptor
B: Mast/stem cell growth factor receptor
C: Kit ligand
D: Kit ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,23510
Polymers141,9084
Non-polymers1,3276
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)269.477, 52.072, 189.791
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mast/stem cell growth factor receptor / SCFR / Proto-oncogene tyrosine-protein kinase Kit / c-kit / CD117 antigen


Mass: 54946.637 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS, D1 - D5 / Mutation: N130S, N145S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIT / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P10721, receptor protein-tyrosine kinase
#2: Protein Kit ligand / Stem cell factor / C-kit ligand / Stem cell factor / SCF / Mast cell growth factor / MGF


Mass: 16007.306 Da / Num. of mol.: 2 / Fragment: Soluble form, residues 26 - 166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCF / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): MGT7 / References: UniProt: P21583
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 8-12% PEG 8000, 5-8% ethylene glycol, 0.2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.249999 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.249999 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 31962 / Num. obs: 31962 / % possible obs: 98.5 % / Redundancy: 3.55 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.9
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 6.6 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EXZ and 2EC8

1exz

2ec8


Resolution: 3.5→38.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4329206.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1594 5 %RANDOM
Rwork0.245 ---
obs0.245 31945 98.3 %-
all-31945 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 243.024 Å2 / ksol: 0.431345 e/Å3
Displacement parametersBiso mean: 78.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.15 Å20 Å228.76 Å2
2--23.73 Å20 Å2
3----16.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3.5→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 84 0 9168
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.411.5
X-RAY DIFFRACTIONc_mcangle_it11.82
X-RAY DIFFRACTIONc_scbond_it11.632
X-RAY DIFFRACTIONc_scangle_it16.822.5
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 241 4.8 %
Rwork0.319 4770 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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