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- PDB-1k5w: THREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 C2B-DOMAIN: SY... -

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Basic information

Entry
Database: PDB / ID: 1k5w
TitleTHREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 C2B-DOMAIN: SYNAPTOTAGMIN 1 AS A PHOSPHOLIPID BINDING MACHINE
ComponentsSynaptotagmin ISynaptotagmin
KeywordsENDOCYTOSIS/EXOCYTOSIS / C2B-DOMAIN / C2-DOMAIN / SYNAPTOTAGMIN I / CALCIUM-BINDING / PHOSPHOLIPID-BINDING / SYNAPSIS / NEUROTRANSMITTER RELEASE / SYNAPTIC VESICLE EXOCYTOSIS / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


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 / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...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 / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / regulation of synaptic vesicle exocytosis / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / 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 / secretory granule / phospholipid binding / terminal bouton / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / 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
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFernandez, I. / Arac, D. / Ubach, J. / Gerber, S.H. / Shin, O. / Gao, Y. / Anderson, R.G.W. / Sudhof, T.C. / Rizo, J.
CitationJournal: Neuron / Year: 2001
Title: Three-dimensional structure of the synaptotagmin 1 C2B-domain: synaptotagmin 1 as a phospholipid binding machine.
Authors: Fernandez, I. / Arac, D. / Ubach, J. / Gerber, S.H. / Shin, O. / Gao, Y. / Anderson, R.G. / Sudhof, T.C. / Rizo, J.
History
DepositionOct 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4323
Polymers17,3521
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500STRUCTURES WITH THE MINIMUM NOE ENERGY
RepresentativeModel #1structure with the minimum noe energy

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Components

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


Mass: 17352.201 Da / Num. of mol.: 1 / Fragment: Residues 270-421, C2B-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 (bacteria) / Strain (production host): BL21 / References: UniProt: P21707
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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
1113D 15N-separated NOESY
121HNHA
1323D-13 15N-SEPARATED NOESY
1441H/13C-HSQC
1533D 15N-separated NOESY
NMR detailsText: STRUCTURE WITH THE MINIMUM NOE ENERGY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.0013M 15N, 13C C2B-Domain50mM Mes 2mM DTT 20mM CaCl2 5%D2O
21.3mM 15N, C2B-Domain50mM Mes 2mM DTT 20mM CaCl2 5%D2O
30.4mM 15N, C2B-Domain50mM Mes 2mM DTT 0.5mM EDTA 5%D2O
41mM 10% 13C, C2B-Domain50mM Mes 2mM DTT 20mM CaCl2 5%D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 6.3 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8DeLaglio et al.processing
VNMR6.1Variancollection
NMRView4.12Johnson, Blevinsdata analysis
CNS0.9Brunger et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 2888 unique, conformationally significant restraints, 2492 are NOE-derived distance constraints, 214 dihedral angle restraints, 170 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: structure with the minimum noe energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE MINIMUM NOE ENERGY
Conformers calculated total number: 500 / Conformers submitted total number: 20

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