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- PDB-8hue: Crystal structure of FGF2-M2 mutant - D28E/C78I/C96I/S137P -

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Basic information

Entry
Database: PDB / ID: 8hue
TitleCrystal structure of FGF2-M2 mutant - D28E/C78I/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 lens fiber cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / response to wortmannin / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / positive regulation of cell fate specification / regulation of retinal cell programmed cell death ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of lens fiber cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / response to wortmannin / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / 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 / negative regulation of fibroblast growth factor receptor signaling pathway / chemokine binding / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / Formation of the nephric duct / positive regulation of epithelial tube formation / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / inner ear auditory receptor cell differentiation / hyaluronan catabolic process / negative regulation of wound healing / positive regulation of stem cell differentiation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / histone H3K9me2/3 reader activity / glial cell differentiation / stem cell development / embryonic morphogenesis / FGFR2b ligand binding and activation / behavioral response to ethanol / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / FGFR1b ligand binding and activation / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / angiogenesis involved in coronary vascular 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 / paracrine signaling / Developmental Lineage of Pancreatic Acinar Cells / positive regulation of blood vessel branching / negative regulation of fibroblast migration / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / endothelial cell proliferation / cell migration involved in sprouting angiogenesis / embryo development ending in birth or egg hatching / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / branching involved in ureteric bud morphogenesis / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / Syndecan interactions / PI-3K cascade:FGFR2 / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / positive regulation of sprouting angiogenesis / chemoattractant activity / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / Non-integrin membrane-ECM interactions / PI3K Cascade / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / response to axon injury / regulation of angiogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / negative regulation of stem cell proliferation / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / neurogenesis
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
sucrose octasulfate / Fibroblast growth factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsJung, Y.E. / Cha, S.S. / An, Y.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos One / Year: 2024
Title: Structural and biochemical investigation into stable FGF2 mutants with novel mutation sites and hydrophobic replacements for surface-exposed cysteines.
Authors: An, Y.J. / Jung, Y.E. / Lee, K.W. / Kaushal, P. / Ko, I.Y. / Shin, S.M. / Ji, S. / Yu, W. / Lee, C. / Lee, W.K. / Cha, K. / Lee, J.H. / Cha, S.S. / Yim, H.S.
History
DepositionDec 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor 2
B: Fibroblast growth factor 2
C: Fibroblast growth factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7995
Polymers49,8333
Non-polymers1,9662
Water6,485360
1
A: Fibroblast growth factor 2


Theoretical massNumber of molelcules
Total (without water)16,6111
Polymers16,6111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5942
Polymers16,6111
Non-polymers9831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fibroblast growth factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5942
Polymers16,6111
Non-polymers9831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.381, 54.446, 71.968
Angle α, β, γ (deg.)90.000, 101.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 3 / 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: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 289.15 K / Method: microbatch
Details: 30% (w/v) polyethylene glycol 2000, 100mM potassium thiocyanate

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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: 1.48→45.48 Å / Num. obs: 64285 / % possible obs: 98.3 % / Redundancy: 5.7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.105 / Net I/σ(I): 26.1
Reflection shellResolution: 1.48→1.51 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3196 / CC1/2: 0.986

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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: 1.48→45.48 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1956 --
Rwork0.1791 --
obs-64268 98.03 %
Displacement parametersBiso mean: 17.31 Å2
Refinement stepCycle: LAST / Resolution: 1.48→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 110 360 3618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213333
X-RAY DIFFRACTIONf_angle_d2.07114514
X-RAY DIFFRACTIONf_chiral_restr0.3589467
X-RAY DIFFRACTIONf_plane_restr0.01560
X-RAY DIFFRACTIONf_dihedral_angle_d25.63241279
LS refinement shellResolution: 1.4758→1.5128 Å
RfactorNum. reflection% reflection
Rfree0.2728 --
Rwork0.2184 --
obs-4221 94 %

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