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- PDB-1bfc: BASIC FIBROBLAST GROWTH FACTOR COMPLEXED WITH HEPARIN HEXAMER FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1bfc
TitleBASIC FIBROBLAST GROWTH FACTOR COMPLEXED WITH HEPARIN HEXAMER FRAGMENT
ComponentsBASIC FIBROBLAST GROWTH FACTOR
KeywordsGROWTH FACTOR / MITOGEN / VASCULARIZATION / HEPARIN-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 neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / response to wortmannin / positive regulation of cell fate specification / regulation of cell migration involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling ...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 / response to wortmannin / positive regulation of cell fate specification / regulation of cell migration involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / 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 / angiogenesis involved in coronary vascular morphogenesis / Formation of the nephric duct / positive regulation of epithelial tube formation / stem cell development / regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cerebellar granule cell precursor proliferation / receptor-receptor interaction / inner ear auditory receptor cell differentiation / negative regulation of wound healing / hyaluronan catabolic process / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / positive regulation of stem cell differentiation / Phospholipase C-mediated cascade; FGFR3 / cerebellar granule cell precursor proliferation / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / embryonic morphogenesis / behavioral response to ethanol / 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 / glial cell differentiation / 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 / embryo development ending in birth or egg hatching / negative regulation of fibroblast migration / positive regulation of blood vessel branching / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / histone H3K9me2/3 reader activity / cell migration involved in sprouting angiogenesis / endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial cell proliferation / 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 / positive regulation of MAP kinase activity / positive regulation of cell division / negative regulation of blood vessel endothelial cell migration / Non-integrin membrane-ECM interactions / PI3K Cascade / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / neuroblast proliferation / regulation of angiogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / response to axon injury / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / negative regulation of stem cell proliferation / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR3 signaling / positive regulation of vascular associated smooth muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease
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 / Resolution: 2.2 Å
AuthorsFaham, S. / Rees, D.C.
Citation
Journal: Science / Year: 1996
Title: Heparin structure and interactions with basic fibroblast growth factor.
Authors: Faham, S. / Hileman, R.E. / Fromm, J.R. / Linhardt, R.J. / Rees, D.C.
#1: Journal: Science / Year: 1991
Title: Three-Dimensional Structures of Acidic and Basic Fibroblast Growth Factors
Authors: Zhu, X. / Komiya, H. / Chirino, A. / Faham, S. / Fox, G.M. / Arakawa, T. / Hsu, B.T. / Rees, D.C.
History
DepositionDec 12, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BASIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2492
Polymers16,5171
Non-polymers1,7321
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.150, 41.800, 85.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BASIC FIBROBLAST GROWTH FACTOR


Mass: 16516.883 Da / Num. of mol.: 1 / Mutation: C70S, C88S / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09038
#2: Polysaccharide 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1732.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a21eEA-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-3/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.69 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlheparin tetrasaccharide1drop
210 mg/mlbFGF1drop
334 %PEG80001reservoir
430 mM1reservoirMgCl2
50.1 MN-[2-acetamido]-2-iminodiacetic acid1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorDetector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 6123 / % possible obs: 94.7 %
Reflection
*PLUS
Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 5481 89.9 %
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms995 0 105 14 1114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.15
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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