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- PDB-4j23: Low resolution crystal structure of the FGFR2D2D3/FGF1/SR128545 c... -

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Basic information

Entry
Database: PDB / ID: 4j23
TitleLow resolution crystal structure of the FGFR2D2D3/FGF1/SR128545 complex
Components
  • Fibroblast growth factor 1
  • Fibroblast growth factor receptor 2
KeywordsSIGNALING PROTEIN/transferase / protein-protein complex / Immunoglobulin C-2 Type / receptor domain / FGF binding / TRANSFERASE / PROTEIN BINDING / MEMBRANE PROTEIN / SIGNALING PROTEIN / SIGNALING PROTEIN-transferase complex
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 / 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 / epidermis morphogenesis / bud elongation involved in lung branching / mesonephric epithelium development / branch elongation involved in ureteric bud branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / regulation of endothelial tube morphogenesis / membranous septum morphogenesis / reproductive structure development / limb bud formation / FGFR3b ligand binding and activation / lung lobe morphogenesis / gland morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / 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 / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / mesenchymal cell proliferation involved in lung development / branching involved in labyrinthine layer morphogenesis / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / embryonic pattern specification / Phospholipase C-mediated cascade; FGFR4 / branching involved in salivary gland morphogenesis / outflow tract septum morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / mesodermal cell differentiation / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / digestive tract development / positive regulation of hepatocyte proliferation / bone morphogenesis / S100 protein binding / skeletal system morphogenesis / odontogenesis / positive regulation of intracellular signal transduction / positive regulation of mesenchymal cell proliferation / ventricular cardiac muscle tissue morphogenesis / ureteric bud development / regulation of osteoblast differentiation / Signaling by FGFR2 IIIa TM / inner ear morphogenesis / midbrain development / organ growth / hair follicle morphogenesis / PI-3K cascade:FGFR3 / lung alveolus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / PI-3K cascade:FGFR2 / bone mineralization / fibroblast growth factor binding / prostate epithelial cord elongation / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR1 / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway / PI3K Cascade
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil ...HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 1 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.882 Å
AuthorsKudlinzki, D. / Saxena, K. / Sreeramulu, S. / Schieborr, U. / Dreyer, M. / Schreuder, H. / Schwalbe, H.
CitationJournal: Cancer Cell / Year: 2013
Title: Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling.
Authors: Herbert, C. / Schieborr, U. / Saxena, K. / Juraszek, J. / De Smet, F. / Alcouffe, C. / Bianciotto, M. / Saladino, G. / Sibrac, D. / Kudlinzki, D. / Sreeramulu, S. / Brown, A. / Rigon, P. / ...Authors: Herbert, C. / Schieborr, U. / Saxena, K. / Juraszek, J. / De Smet, F. / Alcouffe, C. / Bianciotto, M. / Saladino, G. / Sibrac, D. / Kudlinzki, D. / Sreeramulu, S. / Brown, A. / Rigon, P. / Herault, J.P. / Lassalle, G. / Blundell, T.L. / Rousseau, F. / Gils, A. / Schymkowitz, J. / Tompa, P. / Herbert, J.M. / Carmeliet, P. / Gervasio, F.L. / Schwalbe, H. / Bono, F.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Structure summary
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Sep 20, 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_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

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 2
B: Fibroblast growth factor 1


Theoretical massNumber of molelcules
Total (without water)40,6302
Polymers40,6302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-11 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.674, 210.674, 72.512
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 25014.400 Da / Num. of mol.: 1 / Fragment: unp residues 147-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BEK, FGFR2, KGFR, KSAM / Production host: Escherichia coli (E. coli)
References: UniProt: P21802, receptor protein-tyrosine kinase
#2: Protein Fibroblast growth factor 1 / FGF-1 / Acidic fibroblast growth factor / aFGF / Endothelial cell growth factor / ECGF / Heparin- ...FGF-1 / Acidic fibroblast growth factor / aFGF / Endothelial cell growth factor / ECGF / Heparin-binding growth factor 1 / HBGF-1


Mass: 15615.596 Da / Num. of mol.: 1 / Fragment: unp residues 21-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Escherichia coli (E. coli) / References: UniProt: P05230

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.74 Å3/Da / Density % sol: 78.59 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 3.882→182.449 Å / Num. obs: 9212 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 21.4
Reflection shellResolution: 3.882→3.895 Å / Redundancy: 21.5 % / Rmerge(I) obs: 1.352 / Mean I/σ(I) obs: 2.9 / Rsym value: 1.352 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
REFMAC5.5.0102refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DJS

1djs


Resolution: 3.882→39.814 Å / Cor.coef. Fo:Fc: 0.804 / Cor.coef. Fo:Fc free: 0.771 / SU ML: 0.73 / σ(F): 1.34 / Phase error: 49.65 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.384 436 4.75 %
Rwork0.3212 --
obs0.3243 9172 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.761 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å21.47 Å20 Å2
2--2.93 Å20 Å2
3----4.4 Å2
Refinement stepCycle: LAST / Resolution: 3.882→39.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 0 0 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212710
X-RAY DIFFRACTIONf_angle_d2.7383668
X-RAY DIFFRACTIONf_dihedral_angle_d20.715998
X-RAY DIFFRACTIONf_chiral_restr0.107394
X-RAY DIFFRACTIONf_plane_restr0.012471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8822-4.44330.43171310.34632837X-RAY DIFFRACTION100
4.4433-5.59570.42931580.37892873X-RAY DIFFRACTION100
5.5957-39.81570.35691470.29293026X-RAY DIFFRACTION100
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)
17.3177.5943-4.82856.74-4.7591.2613-3.7907-0.5162-1.6121-3.74533.0708-1.7634-2.8669-3.17470.49892.3502-0.4340.22011.1586-0.31271.1991-111.1437-45.507111.6827
28.07860.9515-1.07570.14070.0095-0.0087-4.24585.46670.7272-5.6531-0.11722.35414.66-1.98990.66913.14782.5723-2.6185-6.55285.718-0.9189-111.6371-42.396.1943
37.51924.5185-3.64753.88251.042710.1488-1.829-0.4351-0.6377-0.24470.7385-0.80921.47342.54750.52841.69030.1351-0.16140.3730.17731.226-111.8091-46.073617.4389
40.2799-0.8202-0.26733.53751.01970.8593-0.4158-0.73441.3421-1.0229-0.96671.191-0.9275-0.11491.1753.29970.2679-0.19141.6023-0.18333.0422-96.5843-3.68513.4974
50.22220.36510.35930.2040.27630.38610.180.9665-0.37570.1591-0.3221-0.0054-1.9961.36240.06722.6811-0.1258-0.50071.5991-0.01963.6801-83.69262.96546.8635
65.1044-2.1602-0.18252.51261.2220.8758-2.0088-5.00080.78450.2986-0.80531.1554-0.9577-1.2288-0.07222.7285-0.2625-0.37332.6869-0.53142.7704-84.7193-4.910617.8281
71.23770.05150.80070.71440.48541.70611.2512-1.31730.93192.2079-0.98331.3356-0.951-1.90750.04044.7534-0.3952-0.203-1.1334-0.53983.3709-89.9095.279912.7238
83.2630.7062-1.59253.04964.69172.1213-0.3358-2.12440.0325-0.8728-0.314-2.3054-1.9734-0.31180.76343.19440.0186-0.26381.069-0.14331.346-95.6017-27.694315.9972
93.0257-1.7911-4.67126.59092.06047.8255-0.8178-3.1099-1.65362.92870.095-1.89513.5533-0.14640.22343.2764-0.3902-0.87461.52611.21212.8413-89.7328-33.986123.7189
101.94970.8129-0.83463.0017-0.4910.33231.2674-1.17352.5358-0.5477-1.6224-1.7444-0.6490.1613-0.59155.1308-0.7679-0.9999-0.6394-1.23291.9357-86.236-17.225914.424
118.8621-3.7694-2.58684.05092.10931.2455-1.5704-2.6797-0.30630.4261-0.8635-3.2066-3.29862.94322.07322.8628-0.8699-0.23012.08550.77872.0388-82.0966-24.717219.6423
122.17243.8563.51626.05151.16239.3504-1.8007-0.0065-1.40440.33791.0439-1.0111-2.93971.89990.62042.1817-0.69740.10821.79030.67181.7102-83.2959-26.641310.7805
139.6029-1.728-3.10792.7057-0.35178.7695-0.42511.8502-0.939-2.14070.5515-3.6571-0.28011.64910.80463.52750.42721.43661.28320.37783.5246-77.9448-29.66894.5155
140.3729-1.27370.69954.364-2.3231.21290.2181-1.486-1.1890.42860.46821.060.61190.65590.18841.6448-1.6498-0.5994-4.0987-1.56213.873-85.4851-41.524312.0713
157.4861.05681.81483.4651-2.73683.1824-0.51222.2937-3.3186-1.18720.8799-3.8556-0.0835-0.03610.44352.5270.28880.34011.0057-0.51542.468-85.5223-37.75093.9892
165.42314.3188-5.04394.6557-1.97487.68950.5848-2.65851.1904-0.45661.140.7849-2.2483-1.13960.32340.9271-0.5053-0.94792.06090.39891.4485-99.8507-27.497517.3454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 153:208 )A153 - 208
2X-RAY DIFFRACTION2( CHAIN A AND RESID 209:226 )A209 - 226
3X-RAY DIFFRACTION3( CHAIN A AND RESID 227:249 )A227 - 249
4X-RAY DIFFRACTION4( CHAIN A AND RESID 250:286 )A250 - 286
5X-RAY DIFFRACTION5( CHAIN A AND RESID 287:308 )A287 - 308
6X-RAY DIFFRACTION6( CHAIN A AND RESID 309:326 )A309 - 326
7X-RAY DIFFRACTION7( CHAIN A AND RESID 327:360 )A327 - 360
8X-RAY DIFFRACTION8( CHAIN B AND RESID 22:36 )B22 - 36
9X-RAY DIFFRACTION9( CHAIN B AND RESID 37:58 )B37 - 58
10X-RAY DIFFRACTION10( CHAIN B AND RESID 59:67 )B59 - 67
11X-RAY DIFFRACTION11( CHAIN B AND RESID 68:83 )B68 - 83
12X-RAY DIFFRACTION12( CHAIN B AND RESID 84:114 )B84 - 114
13X-RAY DIFFRACTION13( CHAIN B AND RESID 115:124 )B115 - 124
14X-RAY DIFFRACTION14( CHAIN B AND RESID 125:134 )B125 - 134
15X-RAY DIFFRACTION15( CHAIN B AND RESID 135:146 )B135 - 146
16X-RAY DIFFRACTION16( CHAIN B AND RESID 147:155 )B147 - 155

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