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- PDB-4oeg: Crystal Structure Analysis of FGF2-Disaccharide (S9I2) complex -

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Basic information

Entry
Database: PDB / ID: 4oeg
TitleCrystal Structure Analysis of FGF2-Disaccharide (S9I2) complex
ComponentsFibroblast growth factor 2
KeywordsPROTEIN BINDING / Heparin/Heparin Sulfate Binding
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 / 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 ...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 / 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 / chemokine binding / chondroblast differentiation / lymphatic endothelial cell migration / 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 / positive regulation of epithelial tube formation / Formation of the nephric duct / receptor-receptor interaction / FGFR2b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / paracrine signaling / hyaluronan catabolic process / inner ear auditory receptor cell differentiation / glial cell differentiation / negative regulation of wound healing / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / stem cell development / Phospholipase C-mediated cascade; FGFR3 / embryonic morphogenesis / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / 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 / organ induction / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / negative regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / embryo development ending in birth or egg hatching / endothelial cell proliferation / Signaling by FGFR2 IIIa TM / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / chemoattractant activity / positive regulation of stem cell proliferation / PI-3K cascade:FGFR1 / positive regulation of cell division / negative regulation of blood vessel endothelial cell migration / PI3K Cascade / Non-integrin membrane-ECM interactions / neuroblast proliferation / fibroblast growth factor receptor signaling pathway / response to axon injury / positive regulation of blood vessel endothelial cell migration / canonical Wnt signaling pathway / regulation of angiogenesis / SHC-mediated cascade:FGFR2 / positive regulation of osteoblast differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / negative regulation of stem cell proliferation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / release of sequestered calcium ion into cytosol / FRS-mediated FGFR1 signaling / positive regulation of endothelial cell proliferation / substantia nigra development / Signaling by FGFR1 in disease / regulation of cell migration / ERK1 and ERK2 cascade
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
Fibroblast growth factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, Y.C. / Hsiao, C.D.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Interactions that influence the binding of synthetic heparan sulfate based disaccharides to fibroblast growth factor-2.
Authors: Li, Y.C. / Ho, I.H. / Ku, C.C. / Zhong, Y.Q. / Hu, Y.P. / Chen, Z.G. / Chen, C.Y. / Lin, W.C. / Zulueta, M.M. / Hung, S.C. / Lin, M.G. / Wang, C.C. / Hsiao, C.D.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9392
Polymers17,2501
Non-polymers6901
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.422, 32.994, 35.607
Angle α, β, γ (deg.)65.53, 71.79, 77.00
Int Tables number1
Space group name H-MP1

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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: 17249.732 Da / Num. of mol.: 1 / Fragment: unp residues 134-288 / Mutation: C69S, C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF2, FGFB / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIPL) / References: UniProt: P09038
#2: Polysaccharide 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-1-O-methyl-2-O-sulfo-alpha-L- ...2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-1-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid


Type: oligosaccharide / Mass: 689.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2121A-1a_1-5_1*OC_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO33SO36SO3]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.78 Å3/Da / Density % sol: 30.91 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 40% polyethylene glycol 600 and 100 mM Na2HPO4/citric acid, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 15020 / Num. obs: 15020 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 46.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 19.1 / Rsym value: 0.072 / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BFC

1bfc


Resolution: 1.6→19.641 Å / SU ML: 0.14 / σ(F): 2.06 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1501 10 %RANDOM
Rwork0.171 ---
obs0.1753 15010 94.87 %-
all-15020 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→19.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 41 104 1146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061069
X-RAY DIFFRACTIONf_angle_d1.1111437
X-RAY DIFFRACTIONf_dihedral_angle_d12.178422
X-RAY DIFFRACTIONf_chiral_restr0.07154
X-RAY DIFFRACTIONf_plane_restr0.004177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5963-1.64780.22141310.16221179X-RAY DIFFRACTION91
1.6478-1.70670.20321350.16441213X-RAY DIFFRACTION94
1.7067-1.7750.22281370.16951239X-RAY DIFFRACTION95
1.775-1.85570.2161360.16911230X-RAY DIFFRACTION95
1.8557-1.95340.2281360.17241216X-RAY DIFFRACTION95
1.9534-2.07570.21061390.1671255X-RAY DIFFRACTION96
2.0757-2.23580.22611380.17911232X-RAY DIFFRACTION97
2.2358-2.46040.21341380.17331248X-RAY DIFFRACTION97
2.4604-2.81550.26221400.19211264X-RAY DIFFRACTION97
2.8155-3.54380.21381390.1721243X-RAY DIFFRACTION96
3.5438-19.64240.18731320.15981190X-RAY DIFFRACTION92

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