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- PDB-8om6: Crystal structure of FGF2-STAB, a stable variant of human fibrobl... -

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Basic information

Entry
Database: PDB / ID: 8om6
TitleCrystal structure of FGF2-STAB, a stable variant of human fibroblast growth factor 2
ComponentsFibroblast growth factor 2
KeywordsCYTOKINE / HORMONE/GROWTH FACTOR / MITOGEN
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 / 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 / positive regulation of cell fate specification ...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 / 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 / positive regulation of cell fate specification / 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 / positive regulation of cerebellar granule cell precursor 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 / receptor-receptor interaction / cerebellar granule cell precursor proliferation / inner ear auditory receptor cell differentiation / hyaluronan catabolic process / negative regulation of wound healing / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / positive regulation of stem cell differentiation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / glial cell differentiation / fibroblast growth factor receptor binding / behavioral response to ethanol / embryonic morphogenesis / 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 / Phospholipase C-mediated cascade; FGFR4 / mammary gland epithelial 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 / histone H3K9me2/3 reader activity / embryo development ending in birth or egg hatching / negative regulation of fibroblast migration / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of blood vessel branching / cell migration involved in sprouting angiogenesis / endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial cell proliferation / 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 / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR2 / 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 / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / canonical Wnt signaling pathway / positive regulation of MAP kinase activity / 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 / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling
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
Fibroblast growth factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsMarek, M. / Chaloupkova, R. / de La Bourdonnaye, G.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGA22-09853S Czech Republic
CitationJournal: J Struct Biol X / Year: 2024
Title: Structural analysis of the stable form of fibroblast growth factor 2 - FGF2-STAB.
Authors: de La Bourdonnaye, G. / Marek, M. / Ghazalova, T. / Damborsky, J. / Pachl, P. / Brynda, J. / Stepankova, V. / Chaloupkova, R.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 4, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / pdbx_initial_refinement_model ...atom_site / pdbx_initial_refinement_model / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / struct_conf / struct_conn / struct_keywords / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _refine.pdbx_starting_model / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.2Mar 19, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 2


Theoretical massNumber of molelcules
Total (without water)19,5311
Polymers19,5311
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7100 Å2
Unit cell
Length a, b, c (Å)117.510, 38.670, 34.260
Angle α, β, γ (deg.)90.00, 104.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

21A-326-

HOH

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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: 19531.270 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.93 Å3/Da / Density % sol: 36.2 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: PEG 3350, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.31→33.148 Å / Num. obs: 35777 / % possible obs: 99.37 % / Redundancy: 3.38 % / Rrim(I) all: 0.043 / Net I/σ(I): 15.28
Reflection shellResolution: 1.31→1.357 Å / Mean I/σ(I) obs: 0.75 / Num. unique obs: 3496 / Rrim(I) all: 1.216

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FGF

4fgf


Resolution: 1.31→33.148 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 1788 5 %
Rwork0.1966 --
obs0.1982 35766 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→33.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 0 128 1218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051188
X-RAY DIFFRACTIONf_angle_d0.7991609
X-RAY DIFFRACTIONf_dihedral_angle_d7.308727
X-RAY DIFFRACTIONf_chiral_restr0.082162
X-RAY DIFFRACTIONf_plane_restr0.007212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.34540.39111340.37132551X-RAY DIFFRACTION98
1.3454-1.3850.36391360.34862583X-RAY DIFFRACTION99
1.385-1.42970.35971370.31052606X-RAY DIFFRACTION99
1.4297-1.48080.32031350.27812562X-RAY DIFFRACTION99
1.4808-1.54010.26631360.25692569X-RAY DIFFRACTION99
1.5401-1.61020.26841370.23052636X-RAY DIFFRACTION100
1.6102-1.69510.22351360.21572585X-RAY DIFFRACTION100
1.6951-1.80130.2421400.21682651X-RAY DIFFRACTION100
1.8013-1.94030.23091370.20992607X-RAY DIFFRACTION100
1.9403-2.13560.28111390.21062643X-RAY DIFFRACTION100
2.1356-2.44450.23711380.20672625X-RAY DIFFRACTION100
2.4445-3.07950.22851390.19712642X-RAY DIFFRACTION100
3.0795-33.1480.18161440.15642718X-RAY DIFFRACTION100

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