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- PDB-3caf: Crystal Structure of hFGFR2 D2 Domain -

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Basic information

Entry
Database: PDB / ID: 3caf
TitleCrystal Structure of hFGFR2 D2 Domain
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / FGFR2 / D2 / Fibroblast Growth Factor / ATP-binding / Disease mutation / Ectodermal dysplasia / Glycoprotein / Heparin-binding / Immunoglobulin domain / Kinase / Lacrimo-auriculo-dento-digital syndrome / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase
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 / lateral sprouting from an epithelium / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / 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 / lateral sprouting from an epithelium / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / prostate gland morphogenesis / otic vesicle formation / regulation of smooth muscle cell differentiation / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / endochondral bone growth / morphogenesis of embryonic epithelium / bud elongation involved in lung branching / epidermis morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / reproductive structure development / limb bud formation / membranous septum morphogenesis / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / mesenchymal cell differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / branching involved in labyrinthine layer morphogenesis / mesenchymal cell proliferation involved in lung development / pyramidal neuron development / branching involved in prostate gland morphogenesis / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / regulation of osteoblast proliferation / branching involved in salivary gland morphogenesis / embryonic pattern specification / positive regulation of phospholipase activity / lung-associated mesenchyme development / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / mesodermal cell differentiation / bone morphogenesis / digestive tract development / skeletal system morphogenesis / odontogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / inner ear morphogenesis / organ growth / hair follicle morphogenesis / Signaling by FGFR2 IIIa TM / ventricular cardiac muscle tissue morphogenesis / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of osteoblast differentiation / PI-3K cascade:FGFR2 / lung alveolus development / prostate epithelial cord elongation / midbrain development / bone mineralization / fibroblast growth factor binding / positive regulation of cell division / excitatory synapse / PI3K Cascade / positive regulation of Wnt signaling pathway / cell fate commitment / fibroblast growth factor receptor signaling pathway / epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / embryonic organ development / regulation of ERK1 and ERK2 cascade / SHC-mediated cascade:FGFR2 / positive regulation of cardiac muscle cell proliferation / cellular response to transforming growth factor beta stimulus / FRS-mediated FGFR2 signaling / cellular response to retinoic acid / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell cycle / Signaling by FGFR2 in disease / epithelial cell differentiation / axonogenesis / positive regulation of epithelial cell proliferation / post-embryonic development / animal organ morphogenesis / Negative regulation of FGFR2 signaling / lung development / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity
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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsGuo, F. / Dakshinamurthy, R. / Kathir, K.M. / Thallapuranam, S.K.K. / Sakon, J.
CitationJournal: To be Published
Title: Crystal structure analysis of the hFGFR2 D2 domain
Authors: Guo, F. / Dakshinamurthy, R. / Kathir, K.M. / Thallapuranam, S.K.K. / Sakon, J.
History
DepositionFeb 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)11,6081
Polymers11,6081
Non-polymers00
Water97354
1
A: Fibroblast growth factor receptor 2

A: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)23,2172
Polymers23,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.500, 79.900, 37.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-26-

HOH

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Components

#1: Protein Fibroblast growth factor receptor 2 / FGFR-2 / Keratinocyte growth factor receptor 2 / CD332 antigen


Mass: 11608.258 Da / Num. of mol.: 1 / Fragment: Ig-like C2-type 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KGFR, KSAM / Production host: Escherichia coli (E. coli)
References: UniProt: P21802, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%(w/v) PEG3350, 0.1M (NH3)2SO4, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→16.76 Å / Num. obs: 9401 / % possible obs: 98.1 % / Redundancy: 3.39 % / Rmerge(I) obs: 0.048 / Χ2: 0.98 / Net I/σ(I): 14.4 / Scaling rejects: 242
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.96-2.032.220.3861.917477851.1284.9
2.03-2.112.810.3662.425419011.0296.8
2.11-2.213.460.3083.332989481.0699.8
2.21-2.323.630.243.93445943199.8
2.32-2.473.60.1974.933939350.9599.9
2.47-2.663.630.156.335249640.9100
2.66-2.923.660.0969.934439380.9199.7
2.92-3.343.640.05715.835359700.86100
3.34-4.23.610.03132.635809790.9899.8
4.2-16.763.390.02151.7358710381.1499.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.96 Å16.76 Å
Translation1.96 Å16.76 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→16.76 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.77 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 416 4.9 %RANDOM
Rwork0.187 ---
obs0.191 8479 88.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.551 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.96→16.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 54 868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.021838
X-RAY DIFFRACTIONr_angle_refined_deg2.0821.9211134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.654599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.95823.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78515145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.509156
X-RAY DIFFRACTIONr_chiral_restr0.1810.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02644
X-RAY DIFFRACTIONr_nbd_refined0.2690.2338
X-RAY DIFFRACTIONr_nbtor_refined0.3310.2555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.24
X-RAY DIFFRACTIONr_mcbond_it24.7642515
X-RAY DIFFRACTIONr_mcangle_it23.3743807
X-RAY DIFFRACTIONr_scbond_it2381
X-RAY DIFFRACTIONr_scangle_it87.4863327
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 6 -
Rwork0.276 169 -
all-175 -
obs--25.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
124.122517.00045.708552.84575.44819.41460.5463-0.8995-1.22971.62430.0639-1.351.34930.2244-0.61020.04920.0022-0.0457-0.02590.07110.11655.2-5.96712.585
239.29630.3962-1.418219.5315-9.39044.55310.1252-3.66240.76642.6566-0.4747-0.4251-0.90620.49950.34960.3859-0.1245-0.00610.2168-0.04380.06083.8937.1717.948
332.24570086.689800-0.971-2.5009-0.51373.38231.62590.9132-1.9795-0.4485-0.65490.5482-0.0790.10780.1349-0.08170.17331.76214.99616.447
416.0395-1.5331-8.83783.1162-1.48746.70121.1358-1.09180.39490.9271-0.4074-0.3371-0.4373-0.0197-0.72850.1166-0.07010.00610.099-0.1890.20688.13327.13611.687
532.135231.7047-2.45559.5039-0.15920.3691.1663-2.6007-1.04412.6263-1.1568-1.7466-0.14440.4731-0.00960.07-0.0132-0.01130.1648-0.0976-0.132411.66917.99912.764
60.00030.04790.0287.69684.5032.63450.0696-0.5181-0.76771.0911-0.229-2.0155-0.20370.39090.15930.0374-0.0078-0.12630.02920.05460.180210.1280.43510.237
722.7035-7.4508021.2986019.9769-0.00830.4999-1.1964-1.1527-0.5154-0.49750.3630.36310.5237-0.1435-0.0454-0.0236-0.183-0.0399-0.23588.29212.2491.748
861.78327.92148.177124.57424.575613.06050.37492.5646-1.6802-0.52720.1192-0.25360.22520.9415-0.4941-0.1516-0.01150.005-0.0425-0.0139-0.16557.4715.082-2.876
915.70153.3712-3.194626.49867.453219.0498-0.33051.5601-0.3196-1.02760.6638-0.38990.3202-0.3711-0.3333-0.145-0.04830.04410.0299-0.05380.138216.5719.561-2.467
1013.69183.9409059.7734034.28490.5614-0.2768-0.93143.2053-2.3878-3.5828-1.2512.63971.82640.1919-0.0807-0.05390.0211-0.10840.284118.08714.6366.688
1129.64613.4503039.1544020.5093-0.5915-1.4585-0.55590.30940.665-5.6206-0.37862.4446-0.07360.066-0.0208-0.13080.3060.00210.385715.636.80812.798
122.01230.9790.565610.2495-9.24349.61740.2013-0.13590.62060.1423-0.2909-0.80520.17870.26290.0897-0.0976-0.0246-0.0127-0.0672-0.06470.175213.76823.1696.096
1312.13661.09880.34663.649-0.35758.2933-0.1362-0.10211.15470.16440.06120.0018-0.15620.00660.0751-0.2107-0.02260.0138-0.1411-0.0491-0.17145.07416.9243.768
1417.173212.34142.764779.654515.751619.62680.4040.1301-0.9522-0.9213-0.0364-0.20650.38370.2838-0.3675-0.23150.054-0.0769-0.1434-0.0143-0.02916.032-3.8124.821
156.43061.0479-4.558132.3671000.2251-0.3117-0.548-0.0416-0.3911.0258-0.2816-0.01640.166-0.1567-0.05180.0312-0.151-0.03970.00591.5986.916.818
1616.15269.7132-1.789119.1841-9.65488.80310.535-0.35591.58460.989-0.45542.2534-0.58780.1411-0.0797-0.0857-0.02480.1104-0.0695-0.10830.02734.39324.3598.179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA150 - 1551 - 6
2X-RAY DIFFRACTION2AA156 - 1607 - 11
3X-RAY DIFFRACTION3AA161 - 16512 - 16
4X-RAY DIFFRACTION4AA166 - 17317 - 24
5X-RAY DIFFRACTION5AA174 - 17825 - 29
6X-RAY DIFFRACTION6AA179 - 18930 - 40
7X-RAY DIFFRACTION7AA190 - 19341 - 44
8X-RAY DIFFRACTION8AA194 - 19845 - 49
9X-RAY DIFFRACTION9AA199 - 20550 - 56
10X-RAY DIFFRACTION10AA206 - 21057 - 61
11X-RAY DIFFRACTION11AA211 - 21462 - 65
12X-RAY DIFFRACTION12AA215 - 22566 - 76
13X-RAY DIFFRACTION13AA226 - 23277 - 83
14X-RAY DIFFRACTION14AA233 - 23784 - 88
15X-RAY DIFFRACTION15AA238 - 24389 - 94
16X-RAY DIFFRACTION16AA244 - 24995 - 100

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