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- PDB-6a32: Crystal structure of PDGFRA kinase domain mutant T674I -

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Basic information

Entry
Database: PDB / ID: 6a32
TitleCrystal structure of PDGFRA kinase domain mutant T674I
ComponentsPlatelet-derived growth factor receptor alpha
KeywordsONCOPROTEIN / PDGFRA / T674I / Receptor tyrosine kinase
Function / homology
Function and homology information


Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / platelet-derived growth factor receptor-alpha signaling pathway / platelet-derived growth factor receptor-ligand complex / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization ...Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / platelet-derived growth factor receptor-alpha signaling pathway / platelet-derived growth factor receptor-ligand complex / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / vascular endothelial growth factor binding / embryonic skeletal system morphogenesis / retina vasculature development in camera-type eye / embryonic digestive tract morphogenesis / cardiac myofibril assembly / Leydig cell differentiation / Signaling by PDGF / cell activation / positive regulation of chemotaxis / male genitalia development / embryonic cranial skeleton morphogenesis / phospholipase C activator activity / platelet-derived growth factor receptor binding / estrogen metabolic process / face morphogenesis / signal transduction involved in regulation of gene expression / adrenal gland development / microvillus / platelet-derived growth factor receptor signaling pathway / odontogenesis of dentin-containing tooth / platelet-derived growth factor alpha-receptor activity / roof of mouth development / white fat cell differentiation / negative regulation of platelet activation / vascular endothelial growth factor receptor activity / hematopoietic progenitor cell differentiation / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / transmembrane receptor protein tyrosine kinase activity / extracellular matrix organization / Downstream signal transduction / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / cell chemotaxis / cellular response to reactive oxygen species / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / lung development / wound healing / peptidyl-tyrosine phosphorylation / receptor protein-tyrosine kinase / platelet aggregation / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / cell junction / cell migration / PIP3 activates AKT signaling / protein autophosphorylation / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / in utero embryonic development / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / nuclear body / cilium / positive regulation of cell migration / external side of plasma membrane / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Platelet-derived growth factor receptor alpha / Platelet-derived growth factor receptor Ig-like domain 4 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain ...Platelet-derived growth factor receptor alpha / Platelet-derived growth factor receptor Ig-like domain 4 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin I-set / Immunoglobulin I-set 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/Threonine protein kinases, catalytic domain / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Platelet-derived growth factor receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsYan, X.E. / Liang, L. / Yun, C.H.
CitationJournal: To Be Published
Title: Crystal structure of PDGFRA kinase domain mutant T674I
Authors: Yan, X.E. / Liang, L. / Yun, C.H.
History
DepositionJun 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Platelet-derived growth factor receptor alpha


Theoretical massNumber of molelcules
Total (without water)40,6011
Polymers40,6011
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.194, 87.604, 96.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Platelet-derived growth factor receptor alpha / PDGFR-alpha / Alpha platelet-derived growth factor receptor / Alpha-type platelet-derived growth ...PDGFR-alpha / Alpha platelet-derived growth factor receptor / Alpha-type platelet-derived growth factor receptor / CD140 antigen-like family member A / CD140a antigen / Platelet-derived growth factor alpha receptor / Platelet-derived growth factor receptor 2 / PDGFR-2


Mass: 40600.785 Da / Num. of mol.: 1 / Mutation: T674I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDGFRA, PDGFR2, RHEPDGFRA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P16234, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 5.5, 27% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 26260 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 15.8
Reflection shellHighest resolution: 1.87 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K5X

5k5x


Resolution: 1.87→34.698 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.24 1252 4.77 %
Rwork0.2037 --
obs0.2055 26260 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→34.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 0 93 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112770
X-RAY DIFFRACTIONf_angle_d1.1673743
X-RAY DIFFRACTIONf_dihedral_angle_d22.7521030
X-RAY DIFFRACTIONf_chiral_restr0.098404
X-RAY DIFFRACTIONf_plane_restr0.009468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8703-1.94520.33331210.23772364X-RAY DIFFRACTION85
1.9452-2.03370.2531330.21392701X-RAY DIFFRACTION98
2.0337-2.14090.2771450.20282784X-RAY DIFFRACTION100
2.1409-2.27510.25721360.20152788X-RAY DIFFRACTION100
2.2751-2.45070.25171460.20162821X-RAY DIFFRACTION100
2.4507-2.69720.26781370.20792813X-RAY DIFFRACTION100
2.6972-3.08730.22081560.19912838X-RAY DIFFRACTION100
3.0873-3.88880.22341410.19992860X-RAY DIFFRACTION100
3.8888-34.70350.21261370.20133039X-RAY DIFFRACTION100

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