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- PDB-3dar: Crystal structure of D2 domain from human FGFR2 -

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Basic information

Entry
Database: PDB / ID: 3dar
TitleCrystal structure of D2 domain from human FGFR2
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / IMMUNOGLOBULIN FOLD / ATP-binding / Craniosynostosis / 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 / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / 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 / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / regulation of smooth muscle cell differentiation / orbitofrontal cortex development / regulation of morphogenesis of a branching structure / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / embryonic organ morphogenesis / endochondral bone growth / morphogenesis of embryonic epithelium / epidermis morphogenesis / bud elongation involved in lung branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell differentiation / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation involved in lung development / branching involved in labyrinthine layer morphogenesis / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / embryonic pattern specification / outflow tract septum morphogenesis / positive regulation of phospholipase activity / lung-associated mesenchyme development / mesodermal cell differentiation / digestive tract development / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / bone morphogenesis / skeletal system morphogenesis / odontogenesis / ureteric bud development / positive regulation of mesenchymal cell proliferation / regulation of osteoblast differentiation / ventricular cardiac muscle tissue morphogenesis / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / organ growth / midbrain development / hair follicle morphogenesis / lung alveolus development / fibroblast growth factor binding / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / PI-3K cascade:FGFR2 / bone mineralization / prostate epithelial cord elongation / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway / PI3K Cascade / epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / fibroblast growth factor receptor signaling pathway / embryonic organ development / cell fate commitment / positive regulation of cell cycle / SHC-mediated cascade:FGFR2 / cellular response to retinoic acid / FRS-mediated FGFR2 signaling / positive regulation of cardiac muscle cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / Signaling by FGFR2 in disease / epithelial cell differentiation / axonogenesis / post-embryonic development / regulation of ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / Negative regulation of FGFR2 signaling / animal organ morphogenesis / lung development / bone development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of canonical Wnt signaling pathway
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. / Immunoglobulin subtype ...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 / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsBrown, A. / Blundell, T.L.
CitationJournal: To be Published
Title: Crystal structure of the FGFR2 D2 domain
Authors: Brown, A. / Blundell, T.L.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 10, 2014Group: Refinement description
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)24,3682
Polymers24,3682
Non-polymers00
Water2,198122
1
A: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)12,1841
Polymers12,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)12,1841
Polymers12,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.870, 78.240, 85.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 151 - 249 / Label seq-ID: 7 - 105

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999991, 0.000375, -0.004142), (-0.000457, -0.9998, 0.019971), (-0.004133, 0.019973, 0.999792)20.7999, 9.90785, 0.168978

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Components

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


Mass: 12183.853 Da / Num. of mol.: 2
Fragment: D2 domain, Ig-like C2-type 2, UNP residues 146-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KGFR, KSAM / Plasmid: pBAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P21802, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2006 / Details: Mirrors
RadiationMonochromator: SI(311) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→85.9 Å / Num. all: 14756 / Num. obs: 14667 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.327.40.6231.21529120740.62398.1
2.32-2.467.40.4571.71454719700.45798
2.46-2.637.40.3112.41383718680.31198.6
2.63-2.847.40.1933.71294017470.19398.9
2.84-3.117.40.1225.61214716360.12299.3
3.11-3.487.40.0817.11096114890.08199.2
3.48-4.027.10.05310.8941013270.05399.5
4.02-4.926.60.04511.3741011250.04598.9
4.92-6.967.50.04811.567849070.04899.6
6.96-33.926.70.03116.335095240.03197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.92 Å
Translation2.5 Å33.92 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD Entry 1E0O, chain B, residues 149-249

1e0o


Resolution: 2.2→33.917 Å / FOM work R set: 0.787 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: mlhl
RfactorNum. reflection% reflectionSelection details
Rfree0.255 696 5.06 %random
Rwork0.212 ---
all0.2188 13756 --
obs0.2188 13756 92.31 %-
Solvent computationBsol: 58.254 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 78.28 Å2 / Biso mean: 38.91 Å2 / Biso min: 20.58 Å2
Baniso -1Baniso -2Baniso -3
1--10.247 Å20 Å20 Å2
2--8.643 Å2-0 Å2
3---1.604 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 0 122 1667
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.1491
X-RAY DIFFRACTIONf_bond_d0.0081
X-RAY DIFFRACTIONf_chiral_restr0.0821
X-RAY DIFFRACTIONf_dihedral_angle_d14.4381
X-RAY DIFFRACTIONf_plane_restr0.0051
X-RAY DIFFRACTIONf_nbd_refined4.1261
Refine LS restraints NCSNCS model details: chain B & A / Rms dev position: 0.035 Å
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.2-2.2290.282431X-RAY DIFFRACTION2680
2.229-2.260.262448X-RAY DIFFRACTION2682
2.26-2.2920.255452X-RAY DIFFRACTION2678
2.292-2.3260.264461X-RAY DIFFRACTION2680
2.326-2.3620.253431X-RAY DIFFRACTION2681
2.362-2.4010.257479X-RAY DIFFRACTION2684
2.401-2.4420.238481X-RAY DIFFRACTION2685
2.442-2.4870.247455X-RAY DIFFRACTION2682
2.487-2.5350.232469X-RAY DIFFRACTION2683
2.535-2.5860.225489X-RAY DIFFRACTION2686
2.586-2.6430.22483X-RAY DIFFRACTION2686
2.643-2.7040.251494X-RAY DIFFRACTION2688
2.704-2.7720.228515X-RAY DIFFRACTION2690
2.772-2.8460.218500X-RAY DIFFRACTION2690
2.846-2.930.209489X-RAY DIFFRACTION2686
2.93-3.0250.196521X-RAY DIFFRACTION2691
3.025-3.1330.238523X-RAY DIFFRACTION2692
3.133-3.2580.227530X-RAY DIFFRACTION2692
3.258-3.4060.197533X-RAY DIFFRACTION2693
3.406-3.5860.183542X-RAY DIFFRACTION2694
3.586-3.810.168549X-RAY DIFFRACTION2694
3.81-4.1040.172534X-RAY DIFFRACTION2691
4.104-4.5160.161540X-RAY DIFFRACTION2694
4.516-5.1670.161551X-RAY DIFFRACTION2692
5.167-6.5030.19562X-RAY DIFFRACTION2693
6.503-33.9210.215598X-RAY DIFFRACTION2692

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