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- PDB-2ki6: The FGF1-S100A13-C2A hetero-hexameric complex structure: A compon... -

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Basic information

Entry
Database: PDB / ID: 2ki6
TitleThe FGF1-S100A13-C2A hetero-hexameric complex structure: A component in the non-classical pathway for FGF1 secretion
Components
  • (Protein S100-A13) x 2
  • Heparin-binding growth factor 1
  • Synaptotagmin-1
KeywordsPROTEIN 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 / Acetylcholine Neurotransmitter Release Cycle / syntaxin-3 binding / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion ...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 / Acetylcholine Neurotransmitter Release Cycle / syntaxin-3 binding / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / Serotonin Neurotransmitter Release Cycle / calcium ion sensor activity / Toxicity of botulinum toxin type B (botB) / dense core granule / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / positive regulation of interleukin-1 alpha production / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / vesicle docking / regulation of calcium ion-dependent exocytosis / regulation of endothelial cell chemotaxis to fibroblast growth factor / exocytic vesicle / protein heterooligomerization / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / positive regulation of dopamine secretion / Phospholipase C-mediated cascade; FGFR3 / Glutamate Neurotransmitter Release Cycle / RAGE receptor binding / 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 / neurotransmitter secretion / regulation of exocytosis / positive regulation of dendrite extension / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / neuron projection terminus / calcium-dependent phospholipid binding / Neurexins and neuroligins / positive regulation of hepatocyte proliferation / S100 protein binding / syntaxin-1 binding / low-density lipoprotein particle receptor binding / positive regulation of intracellular signal transduction / syntaxin binding / Signaling by FGFR2 IIIa TM / clathrin binding / mast cell degranulation / phosphatidylserine binding / regulation of dopamine secretion / PI-3K cascade:FGFR3 / fibroblast growth factor binding / PI-3K cascade:FGFR2 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / excitatory synapse / positive regulation of cell division / synaptic vesicle endocytosis / detection of calcium ion / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR3 / positive regulation of synaptic transmission / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / regulation of synaptic transmission, glutamatergic / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / phosphatidylinositol-4,5-bisphosphate binding / Signaling by FGFR2 in disease / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / extracellular matrix / Signaling by FGFR1 in disease / activation of protein kinase B activity
Similarity search - Function
Synaptotagmin / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Cytokine IL1/FGF / C2 domain ...Synaptotagmin / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Cytokine IL1/FGF / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / EF-hand / Recoverin; domain 1 / C2 domain superfamily / EF-hand domain pair / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Fibroblast growth factor 1 / Synaptotagmin-1 / Protein S100-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsKrishna, S.M. / Rani, S.G. / Yu, C.
CitationJournal: 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
DepositionApr 28, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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
C: Protein S100-A13
D: Protein S100-A13
E: Heparin-binding growth factor 1
F: Synaptotagmin-1


Theoretical massNumber of molelcules
Total (without water)82,7816
Polymers82,7816
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 2000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


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 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.: 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 Protein S100-A13 / S100 calcium-binding protein A13


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 Protein S100-A13 / S100 calcium-binding protein A13


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 detailsTHE 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

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The FGF1-S100A13-C2A hetero-hexameric complex structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D-13C-filter NOESY
11213D-15N-filter NOESY
11313D H(CCO)NH
NMR detailsText: C2A(15N&13C labeled) mixed with unlabeled FGF1-S100A13 complex buffer condition (25mM PBD, 100mM NaCl and 2mM CaCl2)

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Sample preparation

DetailsContents: 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
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMC2A domain of Syt1-1[U-100% 13C; U-100% 15N]1
1.0 mMFGF1-21
1.0 mMS100A13-31
1.0 mMS100A13-41
25 mMsodium phosphate-51
100 mMsodium chloride-61
Sample conditionsIonic strength: 0.1 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2 &2.2Linge, O'Donoghue and Nilgesstructure solution
CNSSOLVE1.1 & 1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSSOLVE1.1 & 1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SPARKYGoddardchemical shift assignment
SPARKYGoddarddata analysis
SPARKYGoddardpeak picking
TOPSPIN1.3Bruker Biospincollection
TOPSPIN1.3Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 2000 / Conformers submitted total number: 18 / Representative conformer: 1

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