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- PDB-2lha: Solution structure of C2B with IP6 -

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Basic information

Entry
Database: PDB / ID: 2lha
TitleSolution structure of C2B with IP6
ComponentsSynaptotagmin-1
KeywordsMETAL BINDING PROTEIN / Protein-Drug complex / Beta-sheet protein / Calcium binding protein
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 / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / 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 / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / calcium ion sensor activity / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / dense core granule / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / neurotransmitter secretion / regulation of exocytosis / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / excitatory synapse / synaptic vesicle endocytosis / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / SNARE binding / clathrin-coated endocytic vesicle membrane / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / Clathrin-mediated endocytosis / chemical synaptic transmission / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Synaptotagmin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsJoung, M. / Mohan, S.K. / Yu, C.
CitationJournal: Biochemistry / Year: 2012
Title: Molecular Level Interaction of Inositol Hexaphosphate with the C2B Domain of Human Synaptotagmin I
Authors: Joung, M. / Mohan, S.K. / Yu, C.
History
DepositionAug 8, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Non-polymer description
Revision 1.2Oct 14, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_nmr_software / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_nmr_software.name ..._chem_comp.pdbx_synonyms / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0122
Polymers17,3521
Non-polymers6601
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 17352.201 Da / Num. of mol.: 1 / Fragment: C2B domain, UNP residues 272-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT1, SVP65, SYT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: C2B-IP6 COMPLEX
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HNCA
1613D HBHA(CO)NH
1713D HN(CO)CA
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D (H)CCH-COSY

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] protein-1, 1.1 mM INOSITOL HEXAKISPHOSPHATE-2, 150 mM sodium chloride-3, 20 mM MES-4, 2 mM DTT-5, 2 mM Calcium Chloride-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein-1[U-100% 13C; U-100% 15N]1
1.1 mMINOSITOL HEXAKISPHOSPHATE-21
150 mMsodium chloride-31
20 mMMES-41
2 mMDTT-51
2 mMCalcium Chloride-61
Sample conditionsIonic strength: 0.15 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian varian / Manufacturer: Varian / Model: varian / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
VnmrJVariancollection
VnmrJVarianprocessing
ARIArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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