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- PDB-3gql: Crystal Structure of activated receptor tyrosine kinase in comple... -

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Basic information

Entry
Database: PDB / ID: 3gql
TitleCrystal Structure of activated receptor tyrosine kinase in complex with substrates
ComponentsBasic fibroblast growth factor receptor 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / phosphorylated kinase / activation / ATP analog / ATP-binding / Craniosynostosis / Disease mutation / Disulfide bond / Dwarfism / Glycoprotein / Heparin-binding / Hypogonadotropic hypogonadism / Immunoglobulin domain / Kallmann syndrome / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / receptor-receptor interaction / response to sodium phosphate / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of parathyroid hormone secretion / chordate embryonic development / mesenchymal cell proliferation / paraxial mesoderm development / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / branching involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / outer ear morphogenesis / middle ear morphogenesis / embryonic limb morphogenesis / skeletal system morphogenesis / ureteric bud development / positive regulation of mesenchymal cell proliferation / positive regulation of vascular endothelial cell proliferation / cardiac muscle cell proliferation / inner ear morphogenesis / midbrain development / fibroblast growth factor binding / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / regulation of cell differentiation / PI-3K cascade:FGFR1 / phosphatidylinositol-mediated signaling / PI3K Cascade / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / calcium ion homeostasis / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / positive regulation of phospholipase C activity / SHC-mediated cascade:FGFR1 / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / Signal transduction by L1 / SH2 domain binding / skeletal system development / stem cell proliferation / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / neuron migration / positive regulation of MAP kinase activity / positive regulation of neuron projection development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / cell migration / gene expression / PIP3 activates AKT signaling / heparin binding / cytoplasmic vesicle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / protein tyrosine kinase activity / in utero embryonic development / positive regulation of MAPK cascade / protein autophosphorylation / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / 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 / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / 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
Chem-GQL / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsBae, J.H. / Lew, E.D. / Yuzawa, S. / Tome, F. / Lax, I. / Schlessinger, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: The selectivity of receptor tyrosine kinase signaling is controlled by a secondary SH2 domain binding site.
Authors: Bae, J.H. / Lew, E.D. / Yuzawa, S. / Tome, F. / Lax, I. / Schlessinger, J.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basic fibroblast growth factor receptor 1
B: Basic fibroblast growth factor receptor 1
C: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9666
Polymers111,8733
Non-polymers1,0933
Water3,369187
1
A: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6552
Polymers37,2911
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6552
Polymers37,2911
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6552
Polymers37,2911
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Basic fibroblast growth factor receptor 1
B: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3104
Polymers74,5822
Non-polymers7292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-10 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.168, 78.265, 98.458
Angle α, β, γ (deg.)90.000, 110.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Basic fibroblast growth factor receptor 1 / FGFR-1 / bFGF-R / Fms-like tyrosine kinase 2 / c-fgr


Mass: 37290.871 Da / Num. of mol.: 3 / Fragment: protein kinase domain / Mutation: C488A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFBR, FGFR1, FLG, FLT2 / Production host: Escherichia coli (E. coli)
References: UniProt: P11362, receptor protein-tyrosine kinase
#2: Chemical ChemComp-GQL / (E)-[4-(3,5-difluorophenyl)-3H-pyrrolo[2,3-b]pyridin-3-ylidene](3-methoxyphenyl)methanol


Mass: 364.345 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H14F2N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 277 K / pH: 6.5
Details: PEG 8000, (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 36410 / Observed criterion σ(I): 2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å36.02 Å
Translation3 Å36.02 Å
Phasing dm shellResolution: 3→50 Å / Delta phi final: 0.154 / FOM : 0.158 / Reflection: 26246

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Processing

Software
NameVersionClassificationNB
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→36.01 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.289 1721 4.5 %
Rwork0.252 --
obs0.252 34333 89.8 %
Solvent computationBsol: 35.02 Å2
Displacement parametersBiso mean: 76.37 Å2
Baniso -1Baniso -2Baniso -3
1-6.204 Å20 Å2-9.587 Å2
2---30.813 Å20 Å2
3---24.609 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 81 187 6786
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.22
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4621.5
X-RAY DIFFRACTIONc_mcangle_it2.5492
X-RAY DIFFRACTIONc_scbond_it1.5572
X-RAY DIFFRACTIONc_scangle_it2.4942.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CWATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLX052.PARPLX052.TOP

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