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- PDB-2ec8: Crystal structure of the exctracellular domain of the receptor ty... -

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Basic information

Entry
Database: PDB / ID: 2ec8
TitleCrystal structure of the exctracellular domain of the receptor tyrosine kinase, Kit
ComponentsMast/stem cell growth factor receptor
KeywordsTRANSFERASE / glycoprotein / receptor tyrosine kinase / growth factor cytokine / dimerization
Function / homology
Function and homology information


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 ...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 / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / melanocyte migration / stem cell factor receptor activity / mast cell proliferation / positive regulation of vascular associated smooth muscle cell differentiation / Kit signaling pathway / positive regulation of dendritic cell cytokine production / tongue development / positive regulation of small intestine smooth muscle contraction / positive regulation of mast cell cytokine production / mast cell differentiation / mast cell chemotaxis / Fc receptor signaling pathway / immature B cell differentiation / epithelial cell proliferation / melanocyte differentiation / positive regulation of long-term neuronal synaptic plasticity / primordial germ cell migration / positive regulation of pseudopodium assembly / detection of mechanical stimulus involved in sensory perception of sound / megakaryocyte development / erythropoietin-mediated signaling pathway / somatic stem cell population maintenance / pigmentation / embryonic hemopoiesis / digestive tract development / lamellipodium assembly / Regulation of KIT signaling / stem cell population maintenance / positive regulation of Notch signaling pathway / growth factor binding / positive regulation of tyrosine phosphorylation of STAT protein / Developmental Lineage of Mammary Gland Alveolar Cells / ovarian follicle development / hemopoiesis / cytokine binding / hematopoietic progenitor cell differentiation / T cell differentiation / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / response to cadmium ion / B cell differentiation / stem cell differentiation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / male gonad development / Transcriptional and post-translational regulation of MITF-M expression and activity / visual learning / acrosomal vesicle / SH2 domain binding / erythrocyte differentiation / positive regulation of receptor signaling pathway via JAK-STAT / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / mast cell degranulation / cell chemotaxis / Signaling by SCF-KIT / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cytoplasmic side of plasma membrane / regulation of cell shape / cell-cell junction / actin cytoskeleton organization / PIP3 activates AKT signaling / regulation of cell population proliferation / protein autophosphorylation / cell migration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protease binding / protein tyrosine kinase activity / spermatogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / signaling receptor complex / positive regulation of cell migration / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / protein homodimerization activity / : / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mast/stem cell growth factor receptor Kit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3 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
DepositionFeb 11, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1606
Polymers59,0541
Non-polymers1,1065
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.249, 162.249, 67.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is monomer.

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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: 59054.426 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, D1-D5
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: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 12% PEG 400, 0.2M KCl, 0.1M Na-Pi buffer, pH 6.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 13342 / Num. obs: 13342 / % possible obs: 99.8 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.7
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
REFMAC5.3.0037refinement
RefinementMethod to determine structure: MIRAS / Resolution: 3→27.07 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.866 / SU B: 54.785 / SU ML: 0.464 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29505 650 4.9 %RANDOM
Rwork0.25435 ---
obs0.25638 12521 99.86 %-
all-13189 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0.38 Å20 Å2
2---0.76 Å20 Å2
3---1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 3→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 70 0 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223658
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9685001
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88624.667150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.57115520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5111512
X-RAY DIFFRACTIONr_chiral_restr0.1150.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022756
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3030.21596
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.22467
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3570.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5441.52351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.05623709
X-RAY DIFFRACTIONr_scbond_it3.59631478
X-RAY DIFFRACTIONr_scangle_it5.3344.51292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.001→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 47 -
Rwork0.39 853 -
obs--99.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3685-1.73050.22852.4699-0.16890.08930.08570.0780.1716-0.1564-0.1629-0.15220.03660.03790.07720.2454-0.00320.04170.21490.09450.21114.81119.982820.6287
22.6629-0.81480.70081.4001-0.6730.36720.141-0.2771-0.1299-0.1079-0.08870.0213-0.1589-0.0511-0.05230.28190.0536-0.01720.33630.01420.0353-46.915476.112321.4884
310.3495-4.1168-4.10413.32222.48562.05950.62520.59411.490.22460.0488-0.32660.18110.1402-0.6740.12450.1940.00890.27180.10350.3668-67.531897.825635.4108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 30511 - 305
2X-RAY DIFFRACTION2AA306 - 433306 - 433
3X-RAY DIFFRACTION3AA434 - 508434 - 508
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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