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- PDB-4hwu: Crystal structure of the Ig-C2 type 1 domain from mouse Fibroblas... -

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Basic information

Entry
Database: PDB / ID: 4hwu
TitleCrystal structure of the Ig-C2 type 1 domain from mouse Fibroblast growth factor receptor 2 (FGFR2) [NYSGRC-005912]
ComponentsFibroblast growth factor receptor 2
KeywordsIMMUNE SYSTEM / FGFR2 / KGFR / CD332 / Ig-C2 type 1 domain / Ig superfamily / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


coronal suture morphogenesis / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / FGFR2c ligand binding and activation / FGFR2b ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / urothelial cell proliferation / positive regulation of urothelial cell proliferation / endodermal digestive tract morphogenesis / SHC-mediated cascade:FGFR2 / PI-3K cascade:FGFR2 ...coronal suture morphogenesis / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / FGFR2c ligand binding and activation / FGFR2b ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / urothelial cell proliferation / positive regulation of urothelial cell proliferation / endodermal digestive tract morphogenesis / SHC-mediated cascade:FGFR2 / PI-3K cascade:FGFR2 / FRS-mediated FGFR2 signaling / mesenchymal cell proliferation / lens fiber cell development / fibroblast growth factor receptor apoptotic signaling pathway / PI3K Cascade / mitotic nuclear division / Negative regulation of FGFR2 signaling / epithelial tube branching involved in lung morphogenesis / 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 / vasculogenesis involved in coronary vascular morphogenesis / 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 / membranous septum morphogenesis / reproductive structure development / PIP3 activates AKT signaling / embryonic digestive tract morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / RAF/MAP kinase cascade / organ growth / branching involved in prostate gland morphogenesis / epithelial cell proliferation / mesenchymal cell differentiation / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / negative regulation of mitotic nuclear division / positive regulation of mesenchymal cell proliferation / lung alveolus development / regulation of osteoblast proliferation / stem cell proliferation / fibroblast growth factor receptor activity / embryonic pattern specification / regulation of epithelial cell proliferation / pyramidal neuron development / ureteric bud development / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / hair follicle morphogenesis / post-embryonic development / inner ear morphogenesis / digestive tract development / positive regulation of stem cell proliferation / bone morphogenesis / odontogenesis / bone mineralization / embryonic organ development / midbrain development / fibroblast growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / cell fate commitment / synaptic vesicle transport / positive regulation of cardiac muscle cell proliferation / lung development / canonical Wnt signaling pathway / neuromuscular junction development / cardiac muscle cell proliferation / positive regulation of cell division / ERK1 and ERK2 cascade / fibroblast growth factor binding / regulation of ERK1 and ERK2 cascade / positive regulation of Wnt signaling pathway / stem cell differentiation / axonogenesis / animal organ morphogenesis
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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsKumar, P.R. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. ...Kumar, P.R. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Love, J. / Patel, H. / Rubinstein, R. / Seidel, R. / Stead, M. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of the Ig-C2 type 1 domain from mouse FGFR2 [NYSGRC-005912]
Authors: Kumar, P.R. / Nathenson, S.G. / Almo, S.C.
History
DepositionNov 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Fibroblast growth factor receptor 2
B: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)20,7572
Polymers20,7572
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-10 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.818, 53.818, 122.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer

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Components

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


Mass: 10378.567 Da / Num. of mol.: 2 / Fragment: UNP residues 45-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bek, Ect1, Fgfr2 / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5
References: UniProt: P21803, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (1.1M Malonic acid, 0.15M Ammonium Citrate Tribasic, 0.072M Succinic acid, 0.18M DL-Malic Acid, 0.24M Sodium acetate, 0.3M ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (1.1M Malonic acid, 0.15M Ammonium Citrate Tribasic, 0.072M Succinic acid, 0.18M DL-Malic Acid, 0.24M Sodium acetate, 0.3M Sodium formate, 0.096M Ammonium tartrate dibasic, pH 7.0), Cryoprotection (Reservoir + 20% Glycerol, a speck of I3C (Jena Biosciences) heavy atom), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.5498 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 8822 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.178 / Χ2: 1.3 / Net I/σ(I): 17.75
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.9-2.959.14300.9161100
2.95-310.14550.9221100
3-3.0611.14160.951100
3.06-3.1211.34540.91611000.875
3.12-3.1911.24550.98511000.719
3.19-3.2711.44171.01311000.544
3.27-3.3511.54641.05211000.586
3.35-3.4411.44231.14111000.449
3.44-3.5411.44471.18911000.387
3.54-3.65114301.74511000.469
3.65-3.7810.54332.24811000.28
3.78-3.9411.34521.79311000.25
3.94-4.1111.54441.48411000.166
4.11-4.3311.54301.39211000.137
4.33-4.611.54521.49211000.125
4.6-4.9611.54471.4711000.111
4.96-5.4611.44391.38311000.117
5.46-6.2411.34361.24511000.102
6.24-7.8611.24501.19711000.082
7.86-5011.34481.42111000.057

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.903→46.608 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7795 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 225 4.66 %RANDOM
Rwork0.2265 ---
obs0.2277 4833 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.6 Å2 / Biso mean: 22.2141 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.903→46.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 0 16 1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111192
X-RAY DIFFRACTIONf_angle_d1.4051621
X-RAY DIFFRACTIONf_chiral_restr0.076192
X-RAY DIFFRACTIONf_plane_restr0.007203
X-RAY DIFFRACTIONf_dihedral_angle_d14.4419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9031-3.65740.25311150.22152251236699
3.6574-46.61370.25171100.22862357246798

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