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- PDB-1byn: SOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2-DOMAIN OF SYNAPT... -

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Entry
Database: PDB / ID: 1byn
TitleSOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2-DOMAIN OF SYNAPTOTAGMIN I
ComponentsPROTEIN (SYNAPTOTAGMIN I)
KeywordsENDOCYTOSIS/EXOCYTOSIS / SYNAPTOTAGMIN / C2-DOMAIN / EXOCYTOSIS / NEUROTRANSMITTER RELEASE / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of calcium-dependent activation of synaptic vesicle fusion / vesicle targeting / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / calcium-dependent activation of synaptic vesicle fusion / calcium activated phospholipid scrambling ...regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of calcium-dependent activation of synaptic vesicle fusion / vesicle targeting / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / calcium-dependent activation of synaptic vesicle fusion / calcium activated phospholipid scrambling / chromaffin granule membrane / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / synaptic vesicle recycling / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / calcium ion sensor activity / exocytic vesicle / positive regulation of calcium ion-dependent exocytosis / protein heterooligomerization / vesicle organization / vesicle docking / positive regulation of vesicle fusion / positive regulation of dendrite extension / Cargo recognition for clathrin-mediated endocytosis / calcium-ion regulated exocytosis / Clathrin-mediated endocytosis / vesicle fusion / negative regulation of neurotransmitter secretion / positive regulation of dopamine secretion / calcium-dependent phospholipid binding / dense core granule / xenobiotic transmembrane transport / membraneless organelle assembly / neurotransmitter secretion / syntaxin binding / syntaxin-1 binding / presynaptic active zone / low-density lipoprotein particle receptor binding / phosphatidylserine binding / clathrin binding / regulation of synaptic vesicle exocytosis / neuron projection terminus / inhibitory postsynaptic potential / protein insertion into membrane / regulation of dopamine secretion / regulation of endocytosis / synaptic vesicle exocytosis / detection of calcium ion / postsynaptic cytosol / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / excitatory synapse / cellular response to calcium ion / secretory granule / hippocampal mossy fiber to CA3 synapse / SNARE binding / molecular condensate scaffold activity / phospholipid binding / response to calcium ion / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / presynaptic membrane / cell differentiation / calmodulin binding / postsynaptic membrane / neuron projection / postsynaptic density / protein heterodimerization activity / axon / calcium ion binding / lipid binding / glutamatergic synapse / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsShao, X. / Fernandez, I. / Sudhof, T.C. / Rizo, J.
CitationJournal: Biochemistry / Year: 1998
Title: Solution structures of the Ca2+-free and Ca2+-bound C2A domain of synaptotagmin I: does Ca2+ induce a conformational change?
Authors: Shao, X. / Fernandez, I. / Sudhof, T.C. / Rizo, J.
History
DepositionOct 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SYNAPTOTAGMIN I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9044
Polymers14,7841
Non-polymers1203
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 / 100FEWEST RESTRAINTS VIOLATIONS
Representative

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Components

#1: Protein PROTEIN (SYNAPTOTAGMIN I)


Mass: 14783.882 Da / Num. of mol.: 1 / Fragment: C2A-DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P21707
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D
1213D AND 4D HOMONUCLEAR
131HETERONUCLEAR
141TRIPLE RESONANCE EXPERIMENTS

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Sample preparation

Sample conditionsIonic strength: 100 mM NACL / pH: 5 / Temperature: 307 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY 500 / Manufacturer: Varian / Model: UNITY 500 / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
Discoverstructure solution
NMRCHITECTstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: FEWEST RESTRAINTS VIOLATIONS / Conformers calculated total number: 100 / Conformers submitted total number: 20

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