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- PDB-2bfh: CRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR AT 1.6 ANGSTR... -

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Basic information

Entry
Database: PDB / ID: 2bfh
TitleCRYSTAL STRUCTURE OF BASIC FIBROBLAST GROWTH FACTOR AT 1.6 ANGSTROMS RESOLUTION
ComponentsBASIC FIBROBLAST GROWTH FACTOR
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: 2.5 Å
AuthorsKitagawa, Y. / Ago, H. / Katsube, Y. / Fujishima, A. / Matsuura, Y.
CitationJournal: J.Biochem.(Tokyo) / Year: 1991
Title: Crystal structure of basic fibroblast growth factor at 1.6 A resolution.
Authors: Ago, H. / Kitagawa, Y. / Fujishima, A. / Matsuura, Y. / Katsube, Y.
History
DepositionAug 31, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BASIC FIBROBLAST GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)14,6711
Polymers14,6711
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.380, 34.720, 30.920
Angle α, β, γ (deg.)94.60, 103.50, 87.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein BASIC FIBROBLAST GROWTH FACTOR


Mass: 14670.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P09038
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %bFGF solution1drop
222 %(w/v)PEG40001reservoir
36.1 mM2-mercaptoethanol1reservoir
450 mMsodium citrate 1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. all: 9718 / Num. obs: 4659

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.5→5 Å / σ(F): 3 /
RfactorNum. reflection
obs0.169 3984
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 0 63 1092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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