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- PDB-5a4c: FGFR1 ligand complex -

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Basic information

Entry
Database: PDB / ID: 5a4c
TitleFGFR1 ligand complex
ComponentsFIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
KeywordsTRANSFERASE / KINASE
Function / homology
Function and homology information


Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / cementum mineralization / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / response to sodium phosphate / auditory receptor cell development / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / chordate embryonic development / positive regulation of parathyroid hormone secretion / mesenchymal cell proliferation / paraxial mesoderm development / regulation of postsynaptic density assembly / FGFR1b ligand binding and activation / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / outer ear morphogenesis / embryonic limb morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / skeletal system morphogenesis / positive regulation of mesenchymal cell proliferation / middle ear morphogenesis / ureteric bud development / cardiac muscle cell proliferation / inner ear morphogenesis / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR1 / midbrain development / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / fibroblast growth factor binding / regulation of cell differentiation / PI3K Cascade / cellular response to fibroblast growth factor stimulus / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / epithelial to mesenchymal transition / chondrocyte differentiation / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / positive regulation of MAP kinase activity / positive regulation of neuron differentiation / SH2 domain binding / Signal transduction by L1 / stem cell proliferation / skeletal system development / positive regulation of cell differentiation / stem cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / 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 / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of neuron projection development / neuron migration / neuron projection development / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / cell migration / PIP3 activates AKT signaling / heparin binding
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
Chem-XOJ / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKlein, T. / Vajpai, N. / Phillips, J.J. / Davies, G. / Holdgate, G.A. / Phillips, C. / Tucker, J.A. / Norman, R.A. / Scott, A.S. / Higazi, D.R. ...Klein, T. / Vajpai, N. / Phillips, J.J. / Davies, G. / Holdgate, G.A. / Phillips, C. / Tucker, J.A. / Norman, R.A. / Scott, A.S. / Higazi, D.R. / Lowe, D. / Thompson, G.S. / Breeze, A.L.
CitationJournal: Nat.Commun. / Year: 2015
Title: Structural and Dynamic Insights Into the Energetics of Activation Loop Rearrangement in Fgfr1 Kinase.
Authors: Klein, T. / Vajpai, N. / Phillips, J.J. / Davies, G. / Holdgate, G.A. / Phillips, C. / Tucker, J.A. / Norman, R.A. / Scott, A.D. / Higazi, D.R. / Lowe, D. / Thompson, G.S. / Breeze, A.L.
History
DepositionJun 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,17520
Polymers69,9582
Non-polymers2,21618
Water6,251347
1
A: FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,27912
Polymers34,9791
Non-polymers1,30011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8958
Polymers34,9791
Non-polymers9167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)208.430, 57.460, 65.670
Angle α, β, γ (deg.)90.00, 107.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2103-

HOH

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Components

#1: Protein FIBROBLAST GROWTH FACTOR RECEPTOR 1 (FMS-RELATED TYROSINE KINASE 2, PFEIFFER SYNDROME), ISOFORM CRA_B / FGFR1


Mass: 34979.152 Da / Num. of mol.: 2 / Fragment: RESIDUES 461-765 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11362
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-XOJ / 1-tert-butyl-3-[2-[3-(diethylamino)propylamino]-6-(3,5-dimethoxyphenyl)pyrido[2,3-d]pyrimidin-7-yl]urea


Mass: 509.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H39N7O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.68 Å3/Da / Density % sol: 54.15 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.54
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→99.48 Å / Num. obs: 43082 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 42.71 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.1
Reflection shellResolution: 2.09→2.25 Å / % possible all: 86.7

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→28.73 Å / Cor.coef. Fo:Fc: 0.9508 / Cor.coef. Fo:Fc free: 0.9298 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 2192 5.11 %RANDOM
Rwork0.1944 ---
obs0.1965 42861 96.9 %-
Displacement parametersBiso mean: 50.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.176 Å20 Å21.5331 Å2
2---8.4607 Å20 Å2
3---6.2847 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.09→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 144 347 4963
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014816HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.056584HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1656SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes103HARMONIC2
X-RAY DIFFRACTIONt_gen_planes734HARMONIC5
X-RAY DIFFRACTIONt_it4816HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion17.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion595SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5854SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2588 144 5.81 %
Rwork0.239 2334 -
all0.2402 2478 -
obs--96.9 %
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)
12.3463-0.1685-0.21160.35-0.18381.31630.1960.12670.1397-0.1139-0.08530.0056-0.06140.0878-0.1107-0.13410.02110-0.09160.0466-0.201480.6867-2.625517.3169
23.293-1.08840.14961.14640.27611.20580.23490.48-0.3006-0.0826-0.3080.14730.13780.00720.0731-0.07550.0675-0.05430.0077-0.0592-0.142834.56181.692513.8637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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