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- PDB-2k8m: S100A13-C2A binary complex structure -

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Basic information

Entry
Database: PDB / ID: 2k8m
TitleS100A13-C2A binary complex structure
Components
  • Protein S100-A13
  • Putative uncharacterized protein
KeywordsPROTEIN TRANSPORT / Protein-Protein complex / S100A13 / C2A
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 / Toxicity of botulinum toxin type B (botB) ...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 / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / Acetylcholine Neurotransmitter Release Cycle / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / chromaffin granule membrane / dense core granule / GABA synthesis, release, reuptake and degradation / calcium ion sensor activity / clathrin-sculpted monoamine transport vesicle membrane / calcium ion-regulated exocytosis of neurotransmitter / Serotonin Neurotransmitter Release Cycle / positive regulation of interleukin-1 alpha production / vesicle docking / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / exocytic vesicle / RAGE receptor binding / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / regulation of exocytosis / positive regulation of dendrite extension / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / clathrin binding / mast cell degranulation / fibroblast growth factor binding / phosphatidylserine binding / synaptic vesicle endocytosis / excitatory synapse / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / hippocampal mossy fiber to CA3 synapse / SNARE binding / positive regulation of cytokine production / clathrin-coated endocytic vesicle membrane / synaptic vesicle membrane / calcium-dependent protein binding / protein transport / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / Clathrin-mediated endocytosis / presynaptic membrane / chemical synaptic transmission / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / copper ion binding / axon / lipid binding / glutamatergic synapse / calcium ion binding / positive regulation of cell population proliferation / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Synaptotagmin / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / EF-hand ...Synaptotagmin / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / 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
Synaptotagmin-1 / Synaptotagmin-1 / Protein S100-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMohan, S.K. / Rani, S.G. / Kumar, S.M. / Yu, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: S100A13-C2A binary complex structure-a key component in the acidic fibroblast growth factor for the non-classical pathway.
Authors: Mohan, S.K. / Rani, S.G. / Kumar, S.M. / Yu, C.
History
DepositionSep 14, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Protein S100-A13
C: Protein S100-A13
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)52,5484
Polymers52,5484
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 Putative uncharacterized protein / SYT1


Mass: 14783.882 Da / Num. of mol.: 2 / Fragment: residues 1-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp781D2042, hCG_2016754, SYT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AI31, UniProt: P21579*PLUS
#2: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11490.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99584

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 25 mM [U-100% 15N] sodium phosphate, 100 mM [U-100% 13C] sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphate[U-100% 15N]1
100 mMsodium chloride[U-100% 13C]1
Sample conditionsIonic strength: 0.1 / pH: 5.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2structure solution
CNS1.2refinement
ARIA1.2 & 2.2Linge, O'Donoghue and Nilgesstructure solution
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: ARIA/CNS and 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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