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- PDB-5flf: DISEASE LINKED MUTATION IN FGFR -

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Basic information

Entry
Database: PDB / ID: 5flf
TitleDISEASE LINKED MUTATION IN FGFR
ComponentsFIBROBLAST GROWTH FACTOR RECEPTOR 1
KeywordsTRANSFERASE / AUTO-ACTIVATING / CANCER / GROWTH FACTOR / RECEPTOR / MUTATION
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 / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions / regulation of phosphate transport / FGFR1c and Klotho ligand binding and activation / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway ...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 / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions / regulation of phosphate transport / FGFR1c and Klotho ligand binding and activation / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / vitamin D3 metabolic process / cementum mineralization / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / response to sodium phosphate / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of phospholipase activity / receptor-receptor interaction / chordate embryonic development / positive regulation of parathyroid hormone secretion / auditory receptor cell development / mesenchymal cell proliferation / paraxial mesoderm development / FGFR1b ligand binding and activation / regulation of postsynaptic density assembly / Signaling by activated point mutants of FGFR1 / fibroblast growth factor receptor activity / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / lung-associated mesenchyme development / cell projection assembly / outer ear morphogenesis / embryonic limb morphogenesis / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / ureteric bud development / middle ear morphogenesis / skeletal system morphogenesis / inner ear morphogenesis / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / midbrain development / fibroblast growth factor binding / positive regulation of MAP kinase activity / regulation of cell differentiation / PI3K Cascade / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / cardiac muscle cell proliferation / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / cell maturation / FRS-mediated FGFR1 signaling / cellular response to fibroblast growth factor stimulus / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / SH2 domain binding / peptidyl-tyrosine phosphorylation / stem cell proliferation / Signal transduction by L1 / skeletal system development / stem cell differentiation / positive regulation of cell differentiation / Negative regulation of FGFR1 signaling / sensory perception of sound / positive regulation of neuron projection development / receptor protein-tyrosine kinase / neuron migration / neuron projection development / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / MAPK cascade / heparin binding / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cytoplasmic vesicle / protein tyrosine kinase activity / angiogenesis / gene expression / in utero embryonic development / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / postsynapse / positive regulation of MAPK cascade / positive regulation of cell population proliferation / glutamatergic synapse
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 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ACETATE ION / TRIETHYLENE GLYCOL / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsThiyagarajan, N. / Bunney, T.D. / Katan, M.
CitationJournal: Oncotarget / Year: 2016
Title: Landscape of Activating Cancer Mutations in Fgfr Kinases and Their Differential Responses to Inhibitors in Clinical Use.
Authors: Patani, H. / Bunney, T.D. / Thiyagarajan, N. / Norman, R.A. / Ogg, D. / Breed, J. / Ashford, P. / Potterton, A. / Edwards, M. / Williams, S.V. / Thomson, G.S. / Pang, C.S. / Knowles, M.A. / ...Authors: Patani, H. / Bunney, T.D. / Thiyagarajan, N. / Norman, R.A. / Ogg, D. / Breed, J. / Ashford, P. / Potterton, A. / Edwards, M. / Williams, S.V. / Thomson, G.S. / Pang, C.S. / Knowles, M.A. / Breeze, A.L. / Orengo, C. / Phillips, C. / Katan, M.
History
DepositionOct 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1
C: FIBROBLAST GROWTH FACTOR RECEPTOR 1
D: FIBROBLAST GROWTH FACTOR RECEPTOR 1
E: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,74424
Polymers176,0425
Non-polymers1,70219
Water6,557364
1
A: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3643
Polymers35,2081
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3403
Polymers35,2081
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4904
Polymers35,2081
Non-polymers2823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,24612
Polymers35,2081
Non-polymers1,03711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3052
Polymers35,2081
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.259, 152.281, 195.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
FIBROBLAST GROWTH FACTOR RECEPTOR 1 / FGFR-1 / BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1 / BFGFR / BFGF-R-1 / FMS-LIKE TYROSINE KINASE 2 ...FGFR-1 / BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1 / BFGFR / BFGF-R-1 / FMS-LIKE TYROSINE KINASE 2 / FLT-2 / N-SAM / PROTO-ONCOGENE C-FGR


Mass: 35208.473 Da / Num. of mol.: 5 / Fragment: KINASE DOMAIN, UNP RESIDUES 458-765 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PJ821 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS LAMBDA 37
References: UniProt: P11362, receptor protein-tyrosine kinase

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Non-polymers , 5 types, 383 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.7 Å3/Da / Density % sol: 54.6 % / Description: NONE
Crystal growpH: 7.5
Details: 20 PEG 400, 0.75 M AMMONIUM SULPHATE, 0.1 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→76.26 Å / Num. obs: 70919 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 42.77 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.4
Reflection shellResolution: 2.58→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.5 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UWY

4uwy


Resolution: 2.58→71.064 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.96 / Stereochemistry target values: ML
Details: DISORDERED REGIONS THOSE CANNOT BE OBSERVED WERE DELETED FROM THE MODEL AS THEY AFFECTED THE STATISTICS.
RfactorNum. reflection% reflection
Rfree0.2545 3477 4.9 %
Rwork0.1937 --
obs0.1967 70835 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→71.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11287 0 94 364 11745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311667
X-RAY DIFFRACTIONf_angle_d0.75215763
X-RAY DIFFRACTIONf_dihedral_angle_d13.634456
X-RAY DIFFRACTIONf_chiral_restr0.031730
X-RAY DIFFRACTIONf_plane_restr0.0032009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5801-2.61540.3481430.27992630X-RAY DIFFRACTION96
2.6154-2.65280.37161410.2752652X-RAY DIFFRACTION99
2.6528-2.69240.30651460.26132708X-RAY DIFFRACTION99
2.6924-2.73450.35121400.24982716X-RAY DIFFRACTION99
2.7345-2.77930.3051210.25172695X-RAY DIFFRACTION99
2.7793-2.82720.30061370.25682749X-RAY DIFFRACTION99
2.8272-2.87860.32331430.24782670X-RAY DIFFRACTION99
2.8786-2.9340.34441480.22792735X-RAY DIFFRACTION99
2.934-2.99390.31471310.23782669X-RAY DIFFRACTION98
2.9939-3.0590.2931310.22312612X-RAY DIFFRACTION96
3.059-3.13010.26261460.21982685X-RAY DIFFRACTION99
3.1301-3.20840.27821470.22182709X-RAY DIFFRACTION99
3.2084-3.29520.29681310.22262702X-RAY DIFFRACTION99
3.2952-3.39210.27721450.22482716X-RAY DIFFRACTION98
3.3921-3.50160.30751380.22232699X-RAY DIFFRACTION98
3.5016-3.62680.27121490.1942697X-RAY DIFFRACTION98
3.6268-3.7720.29941300.22032583X-RAY DIFFRACTION94
3.772-3.94360.21071370.17342705X-RAY DIFFRACTION98
3.9436-4.15150.22511550.15732693X-RAY DIFFRACTION98
4.1515-4.41160.17441320.1392725X-RAY DIFFRACTION98
4.4116-4.75210.21191160.14742704X-RAY DIFFRACTION96
4.7521-5.23020.17271400.14682665X-RAY DIFFRACTION96
5.2302-5.98670.25191330.17142736X-RAY DIFFRACTION97
5.9867-7.54130.21691430.17612713X-RAY DIFFRACTION95
7.5413-71.09080.22091540.16832790X-RAY DIFFRACTION94

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