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- PDB-2fgf: THREE-DIMENSIONAL STRUCTURE OF HUMAN BASIC FIBROBLAST GROWTH FACT... -

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Basic information

Entry
Database: PDB / ID: 2fgf
TitleTHREE-DIMENSIONAL STRUCTURE OF HUMAN BASIC FIBROBLAST GROWTH FACTOR, A STRUCTURAL HOMOLOG OF INTERLEUKIN 1BETA
ComponentsHEPARIN-BINDING GROWTH FACTOR 2 PRECURSOR
KeywordsGROWTH FACTOR
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 / negative regulation of wound healing / hyaluronan catabolic process / inner ear auditory receptor cell differentiation / 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: 1.77 Å
AuthorsZhang, J. / Sprang, S.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Three-dimensional structure of human basic fibroblast growth factor, a structural homolog of interleukin 1 beta.
Authors: Zhang, J.D. / Cousens, L.S. / Barr, P.J. / Sprang, S.R.
History
DepositionFeb 19, 1991Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 2 PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7244
Polymers16,4361
Non-polymers2883
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.070, 86.610, 31.930
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 HEPARIN-BINDING GROWTH FACTOR 2 PRECURSOR


Mass: 16435.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P09038
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.77 Å3/Da / Density % sol: 30.49 %
Crystal grow
*PLUS
pH: 5.3 / Method: vapor diffusion / Details: using macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlbFGF1drop
2200 mMsodium succinate1drop
360 mMdithiothreitol1drop
440 %satammonium sulfate1drop
560 %satammonium sulfate1reservoir
6200 mMsodium succinate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 11001 / % possible obs: 97.4 % / Num. measured all: 46630 / Rmerge(I) obs: 0.0456

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.186 / Highest resolution: 1.77 Å
Refinement stepCycle: LAST / Highest resolution: 1.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 15 67 1097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.8
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
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor obs: 0.23 / Lowest resolution: 6 Å / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2.9

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