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- PDB-8hu7: Crystal structure of FGF2-M1 mutant - D28E/C78L/C96I/S137P -

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Basic information

Entry
Database: PDB / ID: 8hu7
TitleCrystal structure of FGF2-M1 mutant - D28E/C78L/C96I/S137P
ComponentsFibroblast growth factor 2
KeywordsSIGNALING PROTEIN / Basic fibroblast growth factor / fibroblast growth factor 2
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / lymphatic endothelial cell migration / chemokine binding / negative regulation of fibroblast growth factor receptor signaling pathway / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / positive regulation of stem cell differentiation / Formation of the nephric duct / positive regulation of epithelial tube formation / hyaluronan catabolic process / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / glial cell differentiation / negative regulation of wound healing / inner ear auditory receptor cell differentiation / stem cell development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / embryonic morphogenesis / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / 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 / mammary gland epithelial cell differentiation / 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 / paracrine signaling / negative regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / embryo development ending in birth or egg hatching / endothelial cell proliferation / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / Signaling by FGFR2 IIIa TM / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR3 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / positive regulation of stem cell proliferation / PI-3K cascade:FGFR4 / chemoattractant activity / PI-3K cascade:FGFR1 / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / Non-integrin membrane-ECM interactions / PI3K Cascade / neuroblast proliferation / response to axon injury / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / canonical Wnt signaling pathway / regulation of angiogenesis / positive regulation of osteoblast differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / negative regulation of stem cell proliferation / release of sequestered calcium ion into cytosol / FRS-mediated FGFR3 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / Signaling by FGFR2 in disease / substantia nigra development / ERK1 and ERK2 cascade / Signaling by FGFR1 in disease / positive regulation of endothelial cell migration / phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF
Similarity search - Domain/homology
Fibroblast growth factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJung, Y.E. / Cha, S.S. / An, Y.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of FGF2-M1 mutant - D28E/C78L/C96I/S137P
Authors: Jung, Y.E. / Cha, S.S. / An, Y.J.
History
DepositionDec 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 2


Theoretical massNumber of molelcules
Total (without water)16,6111
Polymers16,6111
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.375, 54.375, 97.012
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

21A-338-

HOH

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Components

#1: Protein Fibroblast growth factor 2 / FGF-2 / Basic fibroblast growth factor / bFGF / Heparin-binding growth factor 2 / HBGF-2


Mass: 16611.145 Da / Num. of mol.: 1 / Mutation: D28E/C78I/C96I/S137P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF2, FGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P09038
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 289.15 K / Method: microbatch / pH: 5.5
Details: 1.5M sodium citrate, 100mM sodium cacodylate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97941 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.4→47.09 Å / Num. obs: 33205 / % possible obs: 99.76 % / Redundancy: 14.6 % / CC1/2: 1 / Rmerge(I) obs: 0.113 / Net I/σ(I): 64.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 5.2 / Num. unique obs: 3023 / CC1/2: 0.837 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.09 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2127 2003 -
Rwork0.1851 --
obs-33184 99.76 %
Displacement parametersBiso mean: 19.68 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 0 138 1223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01531112
X-RAY DIFFRACTIONf_angle_d1.40481495
X-RAY DIFFRACTIONf_chiral_restr0.1002153
X-RAY DIFFRACTIONf_plane_restr0.011194
X-RAY DIFFRACTIONf_dihedral_angle_d20.8912425
LS refinement shellResolution: 1.4021→1.4371 Å
RfactorNum. reflection% reflection
Rfree0.2212 --
Rwork0.2155 --
obs-2162 98 %

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