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- PDB-2uus: Crystal structure of the rat FGF1-sucrose octasulfate (SOS) complex. -

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Basic information

Entry
Database: PDB / ID: 2uus
TitleCrystal structure of the rat FGF1-sucrose octasulfate (SOS) complex.
ComponentsHEPARIN-BINDING GROWTH FACTOR 1
KeywordsGROWTH FACTOR / DIFFERENTIATION / HEPARIN-BINDING / SUCROSE OCTASULFATE / DEVELOPMENTAL PROTEIN / FIBROBLAST GROWTH FACTOR / MITOGEN / ANGIOGENESIS
Function / homology
Function and homology information


FGFR4 ligand binding and activation / FGFR3b ligand binding and activation / FGFR3c ligand binding and activation / FGFR2c ligand binding and activation / Downstream signaling of activated FGFR1 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling ...FGFR4 ligand binding and activation / FGFR3b ligand binding and activation / FGFR3c ligand binding and activation / FGFR2c ligand binding and activation / Downstream signaling of activated FGFR1 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / FGFR2b ligand binding and activation / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / PI-3K cascade:FGFR2 / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / PI3K Cascade / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / Phospholipase C-mediated cascade; FGFR2 / PIP3 activates AKT signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR2 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / fibroblast growth factor receptor binding / organ induction / positive regulation of hepatocyte proliferation / S100 protein binding / RAF/MAP kinase cascade / positive regulation of sprouting angiogenesis / positive regulation of intracellular signal transduction / positive regulation of cell division / fibroblast growth factor receptor signaling pathway / activation of protein kinase B activity / neurogenesis / Hsp70 protein binding / extracellular matrix / positive regulation of endothelial cell migration / lung development / regulation of cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / growth factor activity / wound healing / positive regulation of cholesterol biosynthetic process / integrin binding / positive regulation of angiogenesis / heparin binding / cellular response to heat / cell cortex / angiogenesis / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus / cytosol / cytoplasm
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
sucrose octasulfate / Fibroblast growth factor 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKulahin, N. / Kiselyov, V. / Kochoyan, A. / Kristensen, O. / Berezin, V. / Bock, E. / Gajhede, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Dimerization Effect of Sucrose Octasulfate on Rat Fgf1.
Authors: Kulahin, N. / Kiselyov, V. / Kochoyan, A. / Kristensen, O. / Kastrup, J.S. / Berezin, V. / Bock, E. / Gajhede, M.
History
DepositionMar 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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

Downloads & links

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Assembly

Deposited unit
A: HEPARIN-BINDING GROWTH FACTOR 1
B: HEPARIN-BINDING GROWTH FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9313
Polymers29,9482
Non-polymers9831
Water2,936163
1
A: HEPARIN-BINDING GROWTH FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9572
Polymers14,9741
Non-polymers9831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HEPARIN-BINDING GROWTH FACTOR 1


Theoretical massNumber of molelcules
Total (without water)14,9741
Polymers14,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.883, 52.778, 73.127
Angle α, β, γ (deg.)90.00, 97.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9993, -0.01496, 0.03432), (-0.01168, 0.9955, 0.09374), (-0.03557, 0.09327, -0.995)
Vector: 13.65, 0.8353, 36.03)

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Components

#1: Protein HEPARIN-BINDING GROWTH FACTOR 1 / HBGF-1 / ACIDIC FIBROBLAST GROWTH FACTOR / AFGF / RAT FGF1 / SUCROSE OCTASULFATE


Mass: 14973.874 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP 10 F' / References: UniProt: P61149
#2: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.7 % / Description: NONE
Crystal growpH: 5 / Details: 10% PEG-6000, 0.1 M CITRIC ACID PH 5.0.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8142
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8142 Å / Relative weight: 1
ReflectionResolution: 2.2→42.68 Å / Num. obs: 14319 / % possible obs: 99.9 % / Observed criterion σ(I): 4.3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J3P

2j3p


Resolution: 2.2→42.68 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / ESU R: 0.349 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 718 5 %RANDOM
Rwork0.206 ---
obs0.21 13571 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.07 Å2
2--0.36 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 55 163 2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212253
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5182.0013063
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8335272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.13524.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.42115394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4081514
X-RAY DIFFRACTIONr_chiral_restr0.1660.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021702
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.2601
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21377
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it12.4081.51323
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.96722128
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it15.6853930
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it15.5424.5932
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.399 56
Rwork0.261 973

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