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

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Basic information

Entry
Database: PDB / ID: 3gqi
TitleCrystal Structure of activated receptor tyrosine kinase in complex with substrates
Components
  • Basic fibroblast growth factor receptor 1
  • Phospholipase C-gamma-1
KeywordsTransferase/Transferase inhibitor / phosphorylated kinase / pY-recognition / tandem SH2 domains / 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 / Hydrolase / Lipid degradation / SH2 domain / SH3 domain / Transducer / Transferase-Transferase Inhibitor COMPLEX
Function / homology
Function and homology information


PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / FCERI mediated Ca+2 mobilization / ISG15 antiviral mechanism ...PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / FCERI mediated Ca+2 mobilization / ISG15 antiviral mechanism / Generation of second messenger molecules / Phospholipase C-mediated cascade; FGFR2 / Downstream signal transduction / Signaling by ALK / Role of phospholipids in phagocytosis / inositol trisphosphate biosynthetic process / DAP12 signaling / VEGFR2 mediated cell proliferation / calcium-dependent phospholipase C activity / Synthesis of IP3 and IP4 in the cytosol / RET signaling / inositol trisphosphate metabolic process / response to curcumin / Signaling by FGFR1 amplification mutants / phosphoinositide phospholipase C / 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 / FCERI mediated MAPK activation / 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 / response to gravity / 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 / phosphatidylinositol metabolic process / 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 / phosphatidylinositol phospholipase C activity / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / COP9 signalosome / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / phospholipase C activity / positive regulation of phospholipase activity / neurotrophin TRKA receptor binding / lung-associated mesenchyme development / cell projection assembly / positive regulation of endothelial cell apoptotic process / phosphatidylinositol-mediated signaling / outer ear morphogenesis / middle ear morphogenesis / embryonic limb morphogenesis / skeletal system morphogenesis / ureteric bud development / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / clathrin-coated vesicle / cardiac muscle cell proliferation / inner ear morphogenesis / midbrain development / positive regulation of epithelial cell migration / fibroblast growth factor binding / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / regulation of cell differentiation / PI-3K cascade:FGFR1 / PI3K Cascade / epithelial to mesenchymal transition / glutamate receptor binding / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / chondrocyte differentiation / positive regulation of phospholipase C activity / SHC-mediated cascade:FGFR1 / release of sequestered calcium ion into cytosol / cell maturation / positive regulation of cardiac muscle cell proliferation / cellular response to epidermal growth factor stimulus / FRS-mediated FGFR1 signaling / ruffle
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Fibroblast growth factor receptor 1, catalytic domain ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Fibroblast growth factor receptor 1, catalytic domain / Phosphatidylinositol-specific phospholipase X-box domain profile. / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Fibroblast growth factor receptor family / SH2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / SHC Adaptor Protein / C2 domain / C2 domain profile. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / SH2 domain superfamily / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / DECAVANADATE / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,2925
Polymers63,8052
Non-polymers1,4873
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.935, 64.596, 94.209
Angle α, β, γ (deg.)90.000, 96.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 37482.742 Da / Num. of mol.: 1 / Fragment: Protein kinase domain / Mutation: C488A, Y583F, C584S, Y575F
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: Protein Phospholipase C-gamma-1 / 1-phosphatidylinositol-4 / 5-bisphosphate phosphodiesterase gamma-1 / Phosphoinositide ...1-phosphatidylinositol-4 / 5-bisphosphate phosphodiesterase gamma-1 / Phosphoinositide phospholipase C / PLC-gamma-1 / PLC-II / PLC-148


Mass: 26322.682 Da / Num. of mol.: 1 / Fragment: tandem SH2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1 / Production host: Escherichia coli (E. coli)
References: UniProt: P10686, phosphoinositide phospholipase C

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Non-polymers , 4 types, 80 molecules

#3: Chemical ChemComp-DVT / DECAVANADATE / Sodium decavanadate


Mass: 957.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O28V10
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEg 8000, taurine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 27448 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Χ2: 1.129
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 31.971 / Num. unique all: 27448 / Χ2: 0.956 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å48.31 Å
Translation3.5 Å48.31 Å
Phasing dm shellResolution: 2.5→50 Å / Delta phi final: 0.177 / FOM : 0.183 / Reflection: 26120

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FGK

1fgk


Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.764 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2608 9.3 %Random
Rwork0.249 ---
all-27940 --
obs-26120 93.5 %-
Solvent computationBsol: 47.058 Å2
Displacement parametersBiso max: 130.76 Å2 / Biso mean: 80.321 Å2 / Biso min: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.929 Å20 Å216.042 Å2
2---16.789 Å20 Å2
3---8.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 70 77 4369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.535
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3acp_DVT_ptr0.paracp_DVT_ptr0.top

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