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- PDB-1rjb: Crystal Structure of FLT3 -

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Basic information

Entry
Database: PDB / ID: 1rjb
TitleCrystal Structure of FLT3
ComponentsFL cytokine receptor
KeywordsTRANSFERASE / Kinase / Autoinhibition / Juxtamembrane domain
Function / homology
Function and homology information


FLT3 mutants bind TKIs / KW2449-resistant FLT3 mutants / semaxanib-resistant FLT3 mutants / crenolanib-resistant FLT3 mutants / gilteritinib-resistant FLT3 mutants / lestaurtinib-resistant FLT3 mutants / midostaurin-resistant FLT3 mutants / pexidartinib-resistant FLT3 mutants / ponatinib-resistant FLT3 mutants / quizartinib-resistant FLT3 mutants ...FLT3 mutants bind TKIs / KW2449-resistant FLT3 mutants / semaxanib-resistant FLT3 mutants / crenolanib-resistant FLT3 mutants / gilteritinib-resistant FLT3 mutants / lestaurtinib-resistant FLT3 mutants / midostaurin-resistant FLT3 mutants / pexidartinib-resistant FLT3 mutants / ponatinib-resistant FLT3 mutants / quizartinib-resistant FLT3 mutants / sorafenib-resistant FLT3 mutants / sunitinib-resistant FLT3 mutants / tandutinib-resistant FLT3 mutants / linifanib-resistant FLT3 mutants / tamatinib-resistant FLT3 mutants / leukocyte homeostasis / lymphocyte proliferation / pro-B cell differentiation / common myeloid progenitor cell proliferation / dendritic cell differentiation / vascular endothelial growth factor receptor activity / phosphatidylinositol 3-kinase activator activity / STAT5 Activation / nuclear glucocorticoid receptor binding / myeloid progenitor cell differentiation / FLT3 signaling through SRC family kinases / cellular response to glucocorticoid stimulus / cytokine receptor activity / STAT5 activation downstream of FLT3 ITD mutants / growth factor binding / cellular response to cytokine stimulus / hemopoiesis / PI3K Cascade / animal organ regeneration / Signaling by FLT3 ITD and TKD mutants / positive regulation of tyrosine phosphorylation of STAT protein / FLT3 signaling by CBL mutants / cell surface receptor protein tyrosine kinase signaling pathway / : / Negative regulation of FLT3 / FLT3 Signaling / transmembrane receptor protein tyrosine kinase activity / B cell differentiation / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / : / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / regulation of apoptotic process / protein tyrosine kinase activity / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome membrane / endoplasmic reticulum lumen / positive regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum / ATP binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain ...Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 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
Receptor-type tyrosine-protein kinase FLT3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGriffith, J. / Black, J. / Faerman, C. / Swenson, L. / Wynn, M. / Lu, F. / Lippke, J. / Saxena, K.
CitationJournal: Mol.Cell / Year: 2004
Title: The structural basis for autoinhibition of FLT3 by the juxtamembrane domain.
Authors: Griffith, J. / Black, J. / Faerman, C. / Swenson, L. / Wynn, M. / Lu, F. / Lippke, J. / Saxena, K.
History
DepositionNov 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FL cytokine receptor


Theoretical massNumber of molelcules
Total (without water)39,7991
Polymers39,7991
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.651, 80.651, 150.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThere is one monomer in the asymmetric unit. The biological unit of construct used is a monomer

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Components

#1: Protein FL cytokine receptor / Tyrosine-protein kinase receptor FLT3 / Stem cell tyrosine kinase 1 / STK-1 / CD135 antigen


Mass: 39799.320 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High-5 Insect Cells / References: UniProt: P36888, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium phosphate, potassium phosphate, CAPS, lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 Msodium phosphate1reservoir
21.2 Mpotassium phosphate1reservoir
31.2 MCAPS1reservoir
40.2 Mlithium sulfate1reservoir
510 mg/mlprotein1drop
62 mMAMP-PNP1drop
74 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 14, 2003 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→29.26 Å / Num. all: 29690 / Num. obs: 29428 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.82 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.23 Å / % possible all: 94.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 29690 / % possible obs: 99.3 %
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
CNX2000refinement
HKL-2000data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1482 5 %RANDOM
Rwork0.21 ---
all0.23 29428 --
obs0.22 29428 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.0478 Å2 / ksol: 0.412735 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å20 Å2
3----3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 0 310 2716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.09
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 230 4.8 %
Rwork0.255 4568 -
obs-4401 99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2WATER_REP.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION4MISSING.DAT&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5PARMXRAY.XPL&_1_TOPOLOGY_INFILE_5
X-RAY DIFFRACTION3&_1_TOPOLOGY_INFILE_3
Refinement
*PLUS
Num. reflection Rfree: 1706 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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