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- PDB-5ui0: Crystal Structure of the Tyrosine Kinase Domain of FGF Receptor 2... -

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Basic information

Entry
Database: PDB / ID: 5ui0
TitleCrystal Structure of the Tyrosine Kinase Domain of FGF Receptor 2 harboring an E565A/K659M Double Gain-of-Function Mutation
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / Tyrosine Kinase Domain / Gain-of-Function Mutation / ATP Analog Cell Surface Receptor
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 / membranous septum morphogenesis / pyramidal neuron development / 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 / digestive tract development / mesodermal cell differentiation / 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 / Signaling by FGFR2 IIIa TM / inner ear morphogenesis / organ growth / midbrain development / hair follicle morphogenesis / lung alveolus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / fibroblast growth factor binding / 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 / negative regulation of keratinocyte proliferation / epithelial to mesenchymal transition / 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 / regulation of ERK1 and ERK2 cascade / post-embryonic development / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / CITRATE ANION / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMohammadi, M. / Chen, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE13686 United States
CitationJournal: Elife / Year: 2017
Title: Elucidation of a four-site allosteric network in fibroblast growth factor receptor tyrosine kinases.
Authors: Chen, H. / Marsiglia, W.M. / Cho, M.K. / Huang, Z. / Deng, J. / Blais, S.P. / Gai, W. / Bhattacharya, S. / Neubert, T.A. / Traaseth, N.J. / Mohammadi, M.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0896
Polymers74,1092
Non-polymers9794
Water4,648258
1
A: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3403
Polymers37,0551
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7493
Polymers37,0551
Non-polymers6942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.937, 73.937, 311.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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


Mass: 37054.559 Da / Num. of mol.: 2 / Fragment: UNP residues 341-651 / Mutation: E565A, K659M
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: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25 mM HEPES pH 7.5, 15%-25% w/v PEG 4000, 0.2-0.3 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 55036 / % possible obs: 98.8 % / Redundancy: 9.1 % / Rsym value: 0.033 / Net I/σ(I): 76.9
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4 % / Mean I/σ(I) obs: 22.6 / Rsym value: 0.086 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PSQ

2psq


Resolution: 2.05→26.141 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 1998 3.64 %
Rwork0.1822 --
obs0.183 54907 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→26.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 62 258 5138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084999
X-RAY DIFFRACTIONf_angle_d0.9696779
X-RAY DIFFRACTIONf_dihedral_angle_d15.393077
X-RAY DIFFRACTIONf_chiral_restr0.06739
X-RAY DIFFRACTIONf_plane_restr0.006869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0499-2.10120.22421340.1763547X-RAY DIFFRACTION95
2.1012-2.1580.21741380.17523659X-RAY DIFFRACTION98
2.158-2.22140.22881420.17583758X-RAY DIFFRACTION100
2.2214-2.29310.22251420.18123752X-RAY DIFFRACTION100
2.2931-2.3750.23511430.18623777X-RAY DIFFRACTION100
2.375-2.470.24331410.18793763X-RAY DIFFRACTION100
2.47-2.58230.20871420.18833766X-RAY DIFFRACTION100
2.5823-2.71830.22261430.19963791X-RAY DIFFRACTION100
2.7183-2.88850.20941430.20513792X-RAY DIFFRACTION100
2.8885-3.11110.23371460.20663838X-RAY DIFFRACTION100
3.1111-3.42360.2211440.19833815X-RAY DIFFRACTION100
3.4236-3.91760.19271460.17433882X-RAY DIFFRACTION100
3.9176-4.93030.17051460.14983863X-RAY DIFFRACTION98
4.9303-26.14280.17881480.1783906X-RAY DIFFRACTION94
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)
10.11840.06240.02340.0620.04670.04760.12860.10460.46770.15170.10460.1622-0.1325-0.2181-0.08610.2472-0.0038-0.00760.18830.07780.387934.98139.882119.5586
20.2026-0.1437-0.16190.07290.07980.1909-0.02680.41980.1548-0.1616-0.00430.1035-0.14430.0939-0.04540.2519-0.0159-0.02370.26840.15180.308144.165635.63358.8877
30.2161-0.168-0.10780.1427-0.01590.06050.0262-0.02130.0876-0.03660.0329-0.04510.08830.0273-00.1560.01390.00150.1580.03060.191440.599530.894520.5739
40.8663-0.16930.03060.3448-0.38120.53350.00670.20480.2708-0.040.0323-0.0319-0.01190.1270.02240.1541-0.02690.00130.22970.02050.214157.194728.701315.6086
51.12220.06240.13940.5298-0.1090.5063-0.0062-0.12090.03090.08130.0311-0.04610.01970.08230.00030.11590.0015-0.01140.2046-0.00870.151761.616320.132229.6227
60.4774-0.0649-0.1240.2161-0.09950.3188-0.054-0.0639-0.2376-0.0650.029-0.19190.14170.0687-00.3080.02770.06520.18830.04290.29643.3503-5.532723.2467
70.3138-0.1814-0.11920.16950.05940.3972-0.0447-0.009-0.0471-0.0243-0.0203-0.12140.0855-0.023200.20870.00990.03880.16240.01280.203938.31140.138923.9087
80.6649-0.04460.21830.2024-0.07670.0274-0.06220.02020.2469-0.3557-0.0457-0.08380.3778-0.0684-0.05540.3230.02990.01280.2645-0.00480.123924.486311.7146-1.9273
90.7617-0.2948-0.12190.97490.12851.0690.00640.1097-0.0288-0.0093-0.06480.09140.0731-0.0965-0.0010.1072-0.00630.00420.1572-0.00990.100919.229812.286221.2801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 461 through 483 )
2X-RAY DIFFRACTION2chain 'A' and (resid 484 through 510 )
3X-RAY DIFFRACTION3chain 'A' and (resid 511 through 541 )
4X-RAY DIFFRACTION4chain 'A' and (resid 542 through 639 )
5X-RAY DIFFRACTION5chain 'A' and (resid 640 through 766 )
6X-RAY DIFFRACTION6chain 'B' and (resid 462 through 510 )
7X-RAY DIFFRACTION7chain 'B' and (resid 511 through 571 )
8X-RAY DIFFRACTION8chain 'B' and (resid 572 through 599 )
9X-RAY DIFFRACTION9chain 'B' and (resid 600 through 765 )

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