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Yorodumi- PDB-2ki6: The FGF1-S100A13-C2A hetero-hexameric complex structure: A compon... -
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-Basic information
Entry | Database: PDB / ID: 2ki6 | ||||||
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Title | The FGF1-S100A13-C2A hetero-hexameric complex structure: A component in the non-classical pathway for FGF1 secretion | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / FGF1-S100A13-C2A hetero-hexameric complex / FGF1 / S100A13 / C2A / Calcium / Cell junction / Cytoplasmic vesicle / Glycoprotein / Lipoprotein / Membrane / Metal-binding / Palmitate / Phosphoprotein / Synapse / Transmembrane / Acetylation / Alternative splicing / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen / Polymorphism | ||||||
Function / homology | Function and homology information clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / 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 / Acetylcholine Neurotransmitter Release Cycle / regulation of regulated secretory pathway ...clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / 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 / Acetylcholine Neurotransmitter Release Cycle / regulation of regulated secretory pathway / calcium ion sensor activity / 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 / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of interleukin-1 alpha production / 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 calcium ion-dependent exocytosis / 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 / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / RAGE 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 / positive regulation of dendrite extension / Phospholipase C-mediated cascade; FGFR4 / regulation of exocytosis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / neurotransmitter secretion / 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 / syntaxin binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / low-density lipoprotein particle receptor binding / clathrin binding / mast cell degranulation / PI-3K cascade:FGFR3 / regulation of dopamine secretion / fibroblast growth factor binding / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / phosphatidylserine binding / PI-3K cascade:FGFR4 / 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 / regulation of synaptic transmission, glutamatergic / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Hsp70 protein binding / Signaling by FGFR2 in disease / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / Signaling by FGFR1 in disease / activation of protein kinase B activity / hippocampal mossy fiber to CA3 synapse Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Krishna, S.M. / Rani, S.G. / Yu, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: The heterohexameric complex structure, a component in the non-classical pathway for fibroblast growth factor 1 (FGF1) secretion. Authors: Mohan, S.K. / Rani, S.G. / Yu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ki6.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2ki6.ent.gz | 3.7 MB | Display | PDB format |
PDBx/mmJSON format | 2ki6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/2ki6 ftp://data.pdbj.org/pub/pdb/validation_reports/ki/2ki6 | HTTPS FTP |
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-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.: 2 / Fragment: C2A domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: purified from heparin affinity column / Gene: SYT1, SVP65, SYT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21579 #2: Protein | Mass: 15118.044 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: purified from GST column / Gene: FGF1, FGFA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05230 #3: Protein | | Mass: 11488.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: purified from GST column / Gene: S100A13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99584 #4: Protein | | Mass: 11489.187 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: purified from GST column / Gene: S100A13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99584 Sequence details | THE CHAIN C AND D ARE S100A13 MONOMERS; BUT IN CHAIN C AND D THE 94, 97 AND 98 RESIDUES ARE ...THE CHAIN C AND D ARE S100A13 MONOMERS; BUT IN CHAIN C AND D THE 94, 97 AND 98 RESIDUES ARE DIFFERENT ISOMERS (DLY OR LYS). | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: The FGF1-S100A13-C2A hetero-hexameric complex structure | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: C2A(15N&13C labeled) mixed with unlabeled FGF1-S100A13 complex buffer condition (25mM PBD, 100mM NaCl and 2mM CaCl2) |
-Sample preparation
Details | Contents: 1.0mM [U-100% 13C; U-100% 15N] C2A domain of Syt1-1, 1.0mM FGF1-2, 1.0mM S100A13-3, S100A13-4, 25mM sodium phosphate-5, 100mM sodium chloride-6, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: CNS | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 2000 / Conformers submitted total number: 18 / Representative conformer: 1 |