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- PDB-1wvz: Solution Structure of the D2 Domain of the Fibroblast Growth Factor -

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Basic information

Entry
Database: PDB / ID: 1wvz
TitleSolution Structure of the D2 Domain of the Fibroblast Growth Factor
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / Fibroblast Growth Factor receptor / heparin / tumor / angiogenesis
Function / homology
Function and homology information


Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development ...Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / prostate gland morphogenesis / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / lacrimal gland development / otic vesicle formation / bud elongation involved in lung branching / regulation of smooth muscle cell differentiation / prostate epithelial cord elongation / lung lobe morphogenesis / regulation of morphogenesis of a branching structure / epithelial cell proliferation involved in salivary gland morphogenesis / branching involved in labyrinthine layer morphogenesis / orbitofrontal cortex development / morphogenesis of embryonic epithelium / branching involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / lung-associated mesenchyme development / epidermis morphogenesis / branching morphogenesis of a nerve / gland morphogenesis / embryonic organ morphogenesis / limb bud formation / endochondral bone growth / membranous septum morphogenesis / reproductive structure development / embryonic digestive tract morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / organ growth / branching involved in prostate gland morphogenesis / mesenchymal cell differentiation / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / FGFR2b ligand binding and activation / positive regulation of phospholipase activity / positive regulation of mesenchymal cell proliferation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / lung alveolus development / Phospholipase C-mediated cascade; FGFR2 / embryonic cranial skeleton morphogenesis / regulation of osteoblast proliferation / fibroblast growth factor receptor activity / embryonic pattern specification / pyramidal neuron development / ureteric bud development / negative regulation of keratinocyte proliferation / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / hair follicle morphogenesis / skeletal system morphogenesis / post-embryonic development / inner ear morphogenesis / digestive tract development / mesodermal cell differentiation / bone morphogenesis / odontogenesis / bone mineralization / embryonic organ development / midbrain development / Signaling by FGFR2 IIIa TM / fibroblast growth factor receptor signaling pathway / regulation of osteoblast differentiation / ventricular cardiac muscle tissue morphogenesis / PI-3K cascade:FGFR2 / cell fate commitment / positive regulation of cardiac muscle cell proliferation / lung development / positive regulation of cell division / fibroblast growth factor binding / epithelial to mesenchymal transition / PI3K Cascade / cellular response to transforming growth factor beta stimulus / regulation of ERK1 and ERK2 cascade / positive regulation of Wnt signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to retinoic acid / SHC-mediated cascade:FGFR2 / axonogenesis / FRS-mediated FGFR2 signaling / animal organ morphogenesis / epithelial cell differentiation / Signaling by FGFR2 in disease / in utero embryonic development / positive regulation of epithelial cell proliferation / positive regulation of cell cycle / peptidyl-tyrosine phosphorylation / excitatory synapse / Negative regulation of FGFR2 signaling / bone development / receptor protein-tyrosine kinase / Constitutive Signaling by Aberrant PI3K in Cancer
Similarity search - Function
Fibroblast growth factor receptor family / 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. ...Fibroblast growth factor receptor family / 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 / 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 / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor receptor 2 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model type detailsminimized average
AuthorsHung, K.W. / Kumar, T.K.S. / Yu, C.
CitationJournal: To be Published
Title: Solution Structure of the D2 Domain of the Fibroblast Growth Factor
Authors: Hung, K.W. / Kumar, T.K.S. / Yu, C.
History
DepositionDec 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)12,0551
Polymers12,0551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #20minimized average structure

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Components

#1: Protein Fibroblast growth factor receptor 2 / FGFR-2 / Keratinocyte growth factor receptor 2


Mass: 12054.738 Da / Num. of mol.: 1 / Fragment: D2 domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UQH9, UniProt: P21802*PLUS, EC: 2.7.1.112
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D NOESY

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Sample preparation

DetailsContents: 1mM Fibroblast Growth Factor Receptor, U-15N, 13C; 20mM phosphate buffer (pH 6.5) containing 20mM NaCl, 50mM ammonium sulfate; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM phosphate buffer containing 20mM NaCl and 50mM ammonium sulfate
pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
CNS3.1structure solution
CNS3.1refinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: the structures are based on a total of 975 are NOE-derived distance constraints, 157 dihedral angle resraints, 39 distance restraints from hydrogen bonds
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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