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- PDB-2d8k: Solution structure of the first C2 domain of synaptotagmin VII -

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Basic information

Entry
Database: PDB / ID: 2d8k
TitleSolution structure of the first C2 domain of synaptotagmin VII
Componentssynaptotagmin VII
KeywordsENDOCYTOSIS/EXOCYTOSIS / exocytosis / calcium binding / lysosome / C2 domain / synaptotagmin / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


calcium ion regulated lysosome exocytosis / vesicle-mediated cholesterol transport / regulation of glucagon secretion / phagosome-lysosome fusion / synaptic vesicle recycling / short-term synaptic potentiation / regulation of bone remodeling / dense core granule / positive regulation of calcium ion-dependent exocytosis / calcium ion-regulated exocytosis of neurotransmitter ...calcium ion regulated lysosome exocytosis / vesicle-mediated cholesterol transport / regulation of glucagon secretion / phagosome-lysosome fusion / synaptic vesicle recycling / short-term synaptic potentiation / regulation of bone remodeling / dense core granule / positive regulation of calcium ion-dependent exocytosis / calcium ion-regulated exocytosis of neurotransmitter / vesicle fusion / plasma membrane repair / regulation of phagocytosis / early phagosome / calcium-dependent phospholipid binding / Neurexins and neuroligins / peroxisomal membrane / syntaxin binding / regulation of synaptic vesicle endocytosis / clathrin binding / phosphatidylserine binding / phagocytosis / phosphatidylinositol-4,5-bisphosphate binding / regulation of insulin secretion / hippocampal mossy fiber to CA3 synapse / SNARE binding / synaptic vesicle membrane / phagocytic vesicle membrane / peroxisome / synaptic vesicle / presynaptic membrane / lysosome / calmodulin binding / lysosomal membrane / axon / calcium ion binding / synapse / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Synaptotagmin 7, C2A domain / Synaptotagmin 7, C2B domain / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like ...Synaptotagmin 7, C2A domain / Synaptotagmin 7, C2B domain / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the first C2 domain of synaptotagmin VII
Authors: Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionDec 6, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: synaptotagmin VII


Theoretical massNumber of molelcules
Total (without water)16,1391
Polymers16,1391
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 / 100target function,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein synaptotagmin VII


Mass: 16139.329 Da / Num. of mol.: 1 / Fragment: C2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: SYT7 / Plasmid: P050620-09 / References: GenBank: 38570146, UniProt: O43581*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.20mM C2 domain U-15N,13C; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.901Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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