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- PDB-2k4a: FGF-1-C2A binary complex structure: a key component in the fibrob... -

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Basic information

Entry
Database: PDB / ID: 2k4a
TitleFGF-1-C2A binary complex structure: a key component in the fibroblast growthfactor non-classical pathway
Components
  • Heparin-binding growth factor 1
  • Synaptotagmin-1
KeywordsPROTEIN TRANSPORT / beta barrel / FGF1-C2A binary complex / Calcium / Cell junction / Cytoplasmic vesicle / Glycoprotein / Lipoprotein / Membrane / Metal-binding / Palmitate / Phosphoprotein / Synapse / Transmembrane / Acetylation / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen / Polymorphism
Function / homology
Function and homology information


Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / clathrin-sculpted acetylcholine transport vesicle membrane / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / regulation of calcium-dependent activation of synaptic vesicle fusion / calcium-dependent activation of synaptic vesicle fusion ...Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / clathrin-sculpted acetylcholine transport vesicle membrane / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / regulation of calcium-dependent activation of synaptic vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / chromaffin granule membrane / : / GABA synthesis, release, reuptake and degradation / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / mesonephric epithelium development / branch elongation involved in ureteric bud branching / calcium activated phospholipid scrambling / Acetylcholine Neurotransmitter Release Cycle / clathrin-sculpted monoamine transport vesicle membrane / regulation of endothelial tube morphogenesis / Serotonin Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / calcium ion sensor activity / synaptic vesicle recycling / Norepinephrine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / protein heterooligomerization / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / exocytic vesicle / Phospholipase C-mediated cascade; FGFR3 / vesicle organization / fibroblast growth factor receptor binding / : / FGFR2b ligand binding and activation / positive regulation of dendrite extension / Glutamate Neurotransmitter Release Cycle / negative regulation of neurotransmitter secretion / regulation of exocytosis / FGFR4 ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / vesicle fusion / positive regulation of dopamine secretion / calcium-dependent phospholipid binding / membraneless organelle assembly / dense core granule / xenobiotic transmembrane transport / S100 protein binding / neurotransmitter secretion / activation of protein kinase B activity / Neurexins and neuroligins / syntaxin-1 binding / presynaptic active zone / Signaling by FGFR2 IIIa TM / inhibitory postsynaptic potential / low-density lipoprotein particle receptor binding / PI-3K cascade:FGFR3 / phosphatidylserine binding / fibroblast growth factor receptor signaling pathway / clathrin binding / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR1 / positive regulation of MAP kinase activity / regulation of synaptic vesicle exocytosis / neuron projection terminus / regulation of endocytosis / protein insertion into membrane / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / detection of calcium ion / postsynaptic cytosol / positive regulation of synaptic transmission / neurogenesis / regulation of synaptic transmission, glutamatergic / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / presynaptic cytosol / FRS-mediated FGFR3 signaling / vesicle-mediated transport / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / phosphatidylinositol-4,5-bisphosphate binding
Similarity search - Function
Synaptotagmin / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain ...Synaptotagmin / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 1 / Synaptotagmin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYu, C. / Mohan, S.K.
CitationJournal: To be Published
Title: FGF-1-C2A binary complex structure: key component in the acidic fibroblast growth factor release
Authors: Mohan, S.K. / Yu, C.
History
DepositionJun 2, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-1
B: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)29,9022
Polymers29,9022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65 / C2A


Mass: 14783.882 Da / Num. of mol.: 1 / Fragment: C2 domain, UNP residues 141-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT1, SVP65, SYT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Protein Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF / Beta-endothelial cell growth factor / ECGF-beta


Mass: 15118.044 Da / Num. of mol.: 1 / Fragment: UNP residues 23-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05230

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 13C(w2)-edited 12C(w2)-filtered NOESY

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Sample preparation

DetailsContents: 1.2mM FGF-1-C2A; 100% D2O / Solvent system: 100% D2O
SampleConc.: 1.2 mM / Component: FGF-1-C2A
Sample conditionsIonic strength: 50mM (NH4)2SO4 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AV800BrukerAV8008001
Bruker AV800BrukerAV80080013C-filter-NOESY

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue, Nilgesstructure solution
HADDOCK2Alexandre Bonvinstructure solution
SparkyGoddardchemical shift assignment
TopSpin1.3Bruker Biospinprocessing
TALOSCornilescu, Delaglio, Baxfor dihedrals
HADDOCK2Alexandre Bonvinrefinement
ARIA/CNSBRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON,WARRENrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: HADDOCK
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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