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- PDB-2erm: Solution structure of a biologically active human FGF-1 monomer, ... -

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Basic information

Entry
Database: PDB / ID: 2erm
TitleSolution structure of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue
ComponentsHeparin-binding growth factor 1
KeywordsHORMONE/GROWTH FACTOR / HEPARIN-LIKE HEXASACCHARIDE / FIBROBLAST GROWTH FACTOR / PROTEIN-CARBOHYDRATE COMPLEX / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / 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 / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of hepatocyte proliferation / S100 protein binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Hsp70 protein binding / Signaling by FGFR2 in disease / extracellular matrix / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / lung development / Negative regulation of FGFR1 signaling / animal organ morphogenesis / growth factor activity / positive regulation of MAP kinase activity / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / cellular response to heat / heparin binding / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / 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
ISOPROPYL ALCOHOL / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Simulated annealing, restrained molecular dynamics
AuthorsCanales, A. / Lozano, R. / Nieto, P.M. / Martin-Lomas, M. / Gimenez-Gallego, G. / Jimenez-Barbero, J.
Citation
Journal: Febs J. / Year: 2006
Title: Solution NMR structure of a human FGF-1 monomer, activated by a hexasaccharide heparin-analogue.
Authors: Canales, A. / Lozano, R. / Lopez-Mendez, B. / Angulo, J. / Ojeda, R. / Nieto, P.M. / Martin-Lomas, M. / Gimenez-Gallego, G. / Jimenez-Barbero, J.
#1: Journal: Biochemistry / Year: 2000
Title: 1H NMR structural characterization of a nonmitogenic, vasodilatory, ischemia-protector and neuromodulatory acidic fibroblast growth factor
Authors: Lozano, R.M. / Pineda-Lucena, A. / Gonzalez, C. / Jimenez, M.A. / Cuevas, P. / Redondo-Horcajo, M. / Sanz, J.M. / Rico, M. / Gimenez-Gallego, G.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Leads for development of new naphthalenesulfonate derivatives with enhanced antiangiogenic activity: crystal structure of acidic fibroblast growth factor in complex with 5-amino-2-naphthalene sulfonate
Authors: Fernandez-Tornero, C. / Lozano, R.M. / Redondo-Horcajo, M. / Gomez, A. / Lopez, J. / Uriel, C. / Valverde, S. / Cuevas, P. / Romero, A. / Gimenez-Gallego, G.
#3: Journal: Proteins / Year: 2004
Title: An atomic resolution structure for human fibroblast growth factor 1
Authors: Bernett, M.J. / Somasundaram, T. / Blaber, M.
#4: Journal: Nature / Year: 1998
Title: Structure of a heparin-linked biologically active dimer of fibroblast growth factor
Authors: DiGabriele, A.D. / Lax, I. / Chen, D.I. / Svahn, C.M. / Jaye, M. / Schlessinger, J. / Hendrickson, W.A.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2433
Polymers15,7111
Non-polymers1,5322
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the lowest energy
RepresentativeModel #20lowest energy

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Components

#1: Protein Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF


Mass: 15710.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: pRAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05230
#2: Polysaccharide 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2- ...2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid


Type: oligosaccharide / Mass: 1472.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,6,5/[a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O][a2121A-1a_1-5][a2122h-1a_1-5_2*NCC/3=O_6*OSO/3=O/3=O]/1-2-3-4-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-IdopA2SO3]{[(4+1)][a-D-GlcpNSO3]{[(4+1)][a-L-IdopA]{[(4+1)][a-D-GlcpNAc6SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO3]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM FGF-1 U-15N; 1 mM heparin-like hexasaccharide; 10mM sodium phosphate; 150 mM sodium chloride; 90% H2O, 10% D2O90% H2O/10% D2O
21 mM FGF-1 U-15N,13C; 1 mM heparin-like hexasaccharide; 10mM sodium phosphate; 150 mM sodium chloride; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.2Brukercollection
VNMR1.1dVariancollection
XEASY1.3.13Bartels C., Xia T., Billeter M., Guntert P., and Wuthrich K.data analysis
DYANA1.5Guntert P., Mumenthaler C., and Wuthrich K.structure solution
Amber5Pearlman D.A., Case D.A., Caldwell J.W., Cheatham T.E., DeBolt S., Ross W.S., Ferguson D., Seibel G.L., and Kollman P.A.refinement
RefinementMethod: Simulated annealing, restrained molecular dynamics / Software ordinal: 1
Details: The first six residues of the protein could not be assigned due to the disorder of the N-terminus region. These are shown as missing residues in remark 465 in all the models. The anomalous ...Details: The first six residues of the protein could not be assigned due to the disorder of the N-terminus region. These are shown as missing residues in remark 465 in all the models. The anomalous torsion angles observed for his 107 and glu 105 are also found in the related pdbs 1dzd and 1dzc of fgf-1. Most of the peptide bonds that deviate significantly from both cis and trans conformation, shown in remark 500, correspond to residues implicated in the binding of the ligand.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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