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- PDB-3jut: Acidic Fibroblast Growth Factor (FGF-1) complexed with gentisic acid -

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Basic information

Entry
Database: PDB / ID: 3jut
TitleAcidic Fibroblast Growth Factor (FGF-1) complexed with gentisic acid
ComponentsHeparin-binding growth factor 1
KeywordsHORMONE / GROWTH FACTOR / FGF-1 INHIBITORS / Angiogenesis / Developmental protein / Differentiation / Heparin-binding / Mitogen
Function / homology
Function and homology information


mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / 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 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / 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 hepatocyte proliferation / S100 protein binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Hsp70 protein binding / Signaling by FGFR2 in disease / extracellular matrix / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / animal organ morphogenesis / lung development / growth factor activity / positive regulation of MAP kinase activity / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / cellular response to heat / heparin binding / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
2,5-dihydroxybenzoic acid / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFernandez, I.S. / Gimenez-Gallego, G. / Romero, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Gentisic acid, a compound associated with plant defense and a metabolite of aspirin, heads a new class of in vivo fibroblast growth factor inhibitors.
Authors: Fernandez, I.S. / Cuevas, P. / Angulo, J. / Lopez-Navajas, P. / Canales-Mayordomo, A. / Gonzalez-Corrochano, R. / Lozano, R.M. / Valverde, S. / Jimenez-Barbero, J. / Romero, A. / Gimenez-Gallego, G.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site
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_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Heparin-binding growth factor 1
B: Heparin-binding growth factor 1
C: Heparin-binding growth factor 1
D: Heparin-binding growth factor 1
E: Heparin-binding growth factor 1
F: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8248
Polymers88,5166
Non-polymers3082
Water41423
1
A: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9072
Polymers14,7531
Non-polymers1541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9072
Polymers14,7531
Non-polymers1541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.658, 47.685, 98.413
Angle α, β, γ (deg.)90.00, 106.45, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41C
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 6 / Auth seq-ID: 1 - 130 / Label seq-ID: 1 - 130

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3DD
4CC
5EE
6FF

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Components

#1: Protein
Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF / Beta-endothelial cell growth factor / ECGF-beta


Mass: 14752.703 Da / Num. of mol.: 6 / Fragment: Heparin-binding, UNP residues 24-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRAT-4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P05230
#2: Chemical ChemComp-GTQ / 2,5-dihydroxybenzoic acid / Gentisic acid


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: Equal volumes of protein and inhibitor solutions, 0.75 and 1.5 mM,respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5 mM sodium phosphate [pH 7.8]. ...Details: Equal volumes of protein and inhibitor solutions, 0.75 and 1.5 mM,respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5 mM sodium phosphate [pH 7.8]. The drops were equilibrated against 200 ml of 1.3M Li2SO4 and typical crystals grew within two weeks , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 7, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.21→47.7 Å / Num. all: 42342 / Num. obs: 41838 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 31.73 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 5.6
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 1.6 / Num. unique all: 5625 / % possible all: 94.6

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1axm

1axm


Resolution: 2.25→37.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.715 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.346 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27406 2034 5.1 %RANDOM
Rwork0.21587 ---
all0.223 41838 --
obs0.21887 38199 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 22 23 6272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0226386
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.9768611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3145773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59724.2300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.168151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.661536
X-RAY DIFFRACTIONr_chiral_restr0.1390.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024854
X-RAY DIFFRACTIONr_nbd_refined0.2220.22268
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24038
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.29
X-RAY DIFFRACTIONr_mcbond_it1.0021.53998
X-RAY DIFFRACTIONr_mcangle_it1.6226205
X-RAY DIFFRACTIONr_scbond_it2.55832751
X-RAY DIFFRACTIONr_scangle_it3.6984.52406
Refine LS restraints NCS

Ens-ID: 1 / Number: 1031 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.635
2Bloose positional0.615
3Dloose positional0.535
4Cloose positional0.535
5Eloose positional0.635
6Floose positional0.725
1Aloose thermal2.5810
2Bloose thermal2.7410
3Dloose thermal2.810
4Cloose thermal3.1610
5Eloose thermal2.6310
6Floose thermal3.6710
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 132 -
Rwork0.275 2818 -
obs--96.28 %
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)
16.4644-0.3747-0.84157.73723.15975.1230.1372-0.3560.07690.5-0.54320.53040.0949-0.81540.406-0.173-0.07870.003-0.1719-0.0638-0.152455.3843-20.873224.3742
25.78120.1156-0.15614.4663-2.08383.6973-0.01320.085-0.1057-0.1837-0.3111-0.13520.11350.59690.3243-0.17190.001-0.0163-0.23490.0022-0.180676.17063.033323.2038
34.40010.9168-0.31434.32640.26277.1665-0.0340.1368-0.0247-0.0238-0.14940.08490.10270.37690.1834-0.21190.02520.0141-0.18110.0012-0.21325.7691-1.186543.6125
46.18972.1846-0.07364.94670.00845.48620.18220.09760.0085-0.0629-0.1423-0.0566-0.41-0.119-0.0399-0.16670.0237-0.0025-0.203-0.0358-0.226769.484522.9628-2.5875
58.2674-1.54790.05823.1688-0.06925.9473-0.04640.031-0.11260.13650.0630.1710.12520.1117-0.0166-0.12490.06440.0113-0.2113-0.0827-0.15192.2766-14.051217.3272
610.17952.5711-2.34144.5202-0.67187.13610.3959-0.9233-0.16340.1484-0.3134-0.2101-0.19360.4373-0.0825-0.1673-0.1237-0.02640.00630.124-0.140531.30339.842528.5983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 130
2X-RAY DIFFRACTION2B1 - 130
3X-RAY DIFFRACTION3D1 - 130
4X-RAY DIFFRACTION4C1 - 130
5X-RAY DIFFRACTION5E1 - 130
6X-RAY DIFFRACTION6F1 - 130

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