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Yorodumi- 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 | ||||||
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Title | FGF-1-C2A binary complex structure: a key component in the fibroblast growthfactor non-classical pathway | ||||||
Components |
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Keywords | PROTEIN 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 clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle ...clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / clathrin-sculpted monoamine transport vesicle membrane / dense core granule / chromaffin granule membrane / calcium ion sensor activity / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / mesonephric epithelium development / calcium ion-regulated exocytosis of neurotransmitter / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / Dopamine Neurotransmitter Release Cycle / FGFR3b ligand binding and activation / Norepinephrine Neurotransmitter Release Cycle / vesicle docking / regulation of endothelial cell chemotaxis to fibroblast growth factor / exocytic vesicle / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / positive regulation of dopamine secretion / protein heterooligomerization / Phospholipase C-mediated cascade; FGFR3 / Glutamate Neurotransmitter Release Cycle / FGFR2b ligand binding and activation / regulation of exocytosis / 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 / positive regulation of dendrite extension / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / neurotransmitter secretion / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / calcium-dependent phospholipid binding / neuron projection terminus / positive regulation of hepatocyte proliferation / Neurexins and neuroligins / S100 protein binding / syntaxin-1 binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / low-density lipoprotein particle receptor binding / clathrin binding / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / phosphatidylserine binding / PI-3K cascade:FGFR1 / positive regulation of cell division / synaptic vesicle endocytosis / excitatory synapse / detection of calcium ion / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / positive regulation of synaptic transmission / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / epithelial cell proliferation / FRS-mediated FGFR1 signaling / regulation of synaptic transmission, glutamatergic / Signaling by FGFR2 in disease / phosphatidylinositol-4,5-bisphosphate binding / Hsp70 protein binding / cellular response to calcium ion / Signaling by FGFR1 in disease / regulation of cell migration / activation of protein kinase B activity / positive regulation of endothelial cell migration / hippocampal mossy fiber to CA3 synapse / extracellular matrix / SNARE binding / lung development / positive regulation of MAP kinase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Yu, C. / Mohan, S.K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k4a.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2k4a.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 2k4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k4a_validation.pdf.gz | 355.2 KB | Display | wwPDB validaton report |
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Full document | 2k4a_full_validation.pdf.gz | 684.3 KB | Display | |
Data in XML | 2k4a_validation.xml.gz | 126.2 KB | Display | |
Data in CIF | 2k4a_validation.cif.gz | 165.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/2k4a ftp://data.pdbj.org/pub/pdb/validation_reports/k4/2k4a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 13C(w2)-edited 12C(w2)-filtered NOESY |
-Sample preparation
Details | Contents: 1.2mM FGF-1-C2A; 100% D2O / Solvent system: 100% D2O |
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Sample | Conc.: 1.2 mM / Component: FGF-1-C2A |
Sample conditions | Ionic strength: 50mM (NH4)2SO4 / pH: 6 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: HADDOCK | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |