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- PDB-3qs7: Crystal structure of a human Flt3 ligand-receptor ternary complex -

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Basic information

Entry
Database: PDB / ID: 3qs7
TitleCrystal structure of a human Flt3 ligand-receptor ternary complex
Components
  • FL cytokine receptor
  • SL cytokine
KeywordsCYTOKINE/SIGNALING PROTEIN / immunoglobulin-like domain / four-helical bundle cytokine / cytokine-receptor complex / extracellular complex / receptor tyrosine kinase / CYTOKINE-SIGNALING PROTEIN complex
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 / common myeloid progenitor cell proliferation / pro-B cell differentiation / lymphocyte proliferation / vascular endothelial growth factor receptor activity / dendritic cell differentiation / nuclear glucocorticoid receptor binding / STAT5 Activation / phosphatidylinositol 3-kinase activator activity / FLT3 signaling through SRC family kinases / myeloid progenitor cell differentiation / cytokine receptor activity / embryonic hemopoiesis / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to glucocorticoid stimulus / growth factor binding / STAT5 activation downstream of FLT3 ITD mutants / cellular response to cytokine stimulus / positive regulation of MAP kinase activity / positive regulation of natural killer cell proliferation / hemopoiesis / PI3K Cascade / Signaling by FLT3 ITD and TKD mutants / FLT3 signaling by CBL mutants / transmembrane receptor protein tyrosine kinase activity / liver regeneration / FLT3 Signaling / Negative regulation of FLT3 / cell surface receptor protein tyrosine kinase signaling pathway / peptidyl-tyrosine phosphorylation / B cell differentiation / cytokine activity / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome membrane / positive regulation of MAPK cascade / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / protein-containing complex binding / cell surface / endoplasmic reticulum / signal transduction / extracellular space / extracellular region / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Flt3 ligand / flt3 ligand / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Four-helical cytokine-like, core / Immunoglobulin / Immunoglobulin domain / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Flt3 ligand / flt3 ligand / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Four-helical cytokine-like, core / Immunoglobulin / Immunoglobulin domain / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Similarity search - Domain/homology
Receptor-type tyrosine-protein kinase FLT3 / Fms-related tyrosine kinase 3 ligand
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.3 Å
AuthorsVerstraete, K. / Savvides, S.N.
Citation
Journal: Blood / Year: 2011
Title: Structural insights into the extracellular assembly of the hematopoietic Flt3 signaling complex.
Authors: Verstraete, K. / Vandriessche, G. / Januar, M. / Elegheert, J. / Shkumatov, A.V. / Desfosses, A. / Van Craenenbroeck, K. / Svergun, D.I. / Gutsche, I. / Vergauwen, B. / Savvides, S.N.
#1: Journal: To be Published
Title: Inducible production of human Flt3 ectodomain variants in mammalian cells and preliminary crystallographic analysis of Flt3 ligand-receptor complexes
Authors: Verstraete, K. / Vandriessche, G. / Januar, M. / Elegheert, J. / Shkumatov, A. / Desfosses, A. / Van Craenenbroeck, K. / Svergun, D. / Gutsche, I. / Vergauwen, B. / Savvides, S.N.
#2: Journal: Protein J. / Year: 2009
Title: Efficient production of bioactive recombinant human Flt3 ligand in E. coli.
Authors: Verstraete, K. / Koch, S. / Ertugrul, S. / Vandenberghe, I. / Aerts, M. / Vandriessche, G. / Thiede, C. / Savvides, S.N.
History
DepositionFeb 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Sep 13, 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
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SL cytokine
B: SL cytokine
C: SL cytokine
D: SL cytokine
E: FL cytokine receptor
F: FL cytokine receptor
G: FL cytokine receptor
H: FL cytokine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,43815
Polymers255,8908
Non-polymers1,5487
Water00
1
A: SL cytokine
B: SL cytokine
E: FL cytokine receptor
F: FL cytokine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8308
Polymers127,9454
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SL cytokine
D: SL cytokine
G: FL cytokine receptor
H: FL cytokine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6087
Polymers127,9454
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-12 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.890, 146.260, 105.950
Angle α, β, γ (deg.)90.000, 109.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SL cytokine / Flt3 ligand / Fms-related tyrosine kinase 3 ligand / Flt3L


Mass: 15873.217 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 27-160)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLT3LG / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA-GAMI(DE3) / References: UniProt: P49771
#2: Protein
FL cytokine receptor / Tyrosine-protein kinase receptor FLT3 / Fms-like tyrosine kinase 3 / FLT-3 / Stem cell tyrosine ...Tyrosine-protein kinase receptor FLT3 / Fms-like tyrosine kinase 3 / FLT-3 / Stem cell tyrosine kinase 1 / STK-1


Mass: 48099.188 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 27-436)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLT3, STK1 / Plasmid: pcDNA4/TO / Cell line (production host): HEK 293 GNTI- / Production host: Homo sapiens (human)
References: UniProt: P36888, receptor protein-tyrosine kinase
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 11-13% PEG4000, 0.1 M magnesium chloride, 50 mM MES, 5 mg/mL Flt3 ligand-receptor complex, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9714
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9714 Å / Relative weight: 1
ReflectionResolution: 4.3→40 Å / Num. all: 20434 / Num. obs: 20184 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 135 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 12.04
Reflection shellResolution: 4.3→4.45 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.08 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ETE AND 2E9W

1ete

2e9w


Resolution: 4.3→39.04 Å / Cor.coef. Fo:Fc: 0.8832 / Cor.coef. Fo:Fc free: 0.8516 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 1010 5 %RANDOM
Rwork0.2604 ---
obs0.2614 20182 98.8 %-
all-20434 --
Displacement parametersBiso max: 242.95 Å2 / Biso mean: 168.8768 Å2 / Biso min: 122.08 Å2
Baniso -1Baniso -2Baniso -3
1-8.4999 Å20 Å2-12.041 Å2
2--13.4404 Å20 Å2
3----21.9403 Å2
Refine analyzeLuzzati coordinate error obs: 1.374 Å
Refinement stepCycle: LAST / Resolution: 4.3→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10767 0 98 0 10865
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111131HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1215385HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion2.45
X-RAY DIFFRACTIONt_dihedral_angle_d4711SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes114HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1808HARMONIC5
X-RAY DIFFRACTIONt_it11131HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion1717SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance469HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact12344SEMIHARMONIC4
LS refinement shellResolution: 4.3→4.53 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2675 141 4.86 %
Rwork0.2677 2763 -
all0.2677 2904 -
obs-2763 -

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