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- PDB-1ugk: Solution structure of the first C2 domain of synaptotagmin IV fro... -

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Entry
Database: PDB / ID: 1ugk
TitleSolution structure of the first C2 domain of synaptotagmin IV from human fetal brain (KIAA1342)
ComponentsSynaptotagmin IV
KeywordsPROTEIN BINDING / BETA SANDWICH / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / negative regulation of short-term neuronal synaptic plasticity / vesicle fusion with vesicle / secretory granule maturation / negative regulation of dense core granule exocytosis / positive regulation of dense core granule exocytosis / negative regulation of retrograde trans-synaptic signaling by neuropeptide / dense core granule membrane / negative regulation of catecholamine secretion / negative regulation of vesicle fusion ...: / negative regulation of short-term neuronal synaptic plasticity / vesicle fusion with vesicle / secretory granule maturation / negative regulation of dense core granule exocytosis / positive regulation of dense core granule exocytosis / negative regulation of retrograde trans-synaptic signaling by neuropeptide / dense core granule membrane / negative regulation of catecholamine secretion / negative regulation of vesicle fusion / : / : / microvesicle / dense core granule cytoskeletal transport / syntaxin-3 binding / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / regulation of calcium ion-dependent exocytosis / exocytic vesicle / negative regulation of calcium ion-dependent exocytosis / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / astrocyte projection / neurotransmitter secretion / positive regulation of dendrite extension / calcium-dependent phospholipid binding / neuron projection terminus / positive regulation of glutamate secretion / syntaxin-1 binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / neuronal dense core vesicle / regulation of endocytosis / negative regulation of protein secretion / vesicle-mediated transport / cellular response to calcium ion / SNARE binding / brain development / memory / neuron projection / protein heterodimerization activity / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / synapse / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / plasma membrane
Similarity search - Function
Synaptotagmin-4 / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNagashima, T. / Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. ...Nagashima, T. / Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Ohara, O. / Nagase, T. / Kikuno, R. / Nakayama, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the first C2 domain of synaptotagmin IV from human fetal brain (KIAA1342)
Authors: Nagashima, T. / Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / ...Authors: Nagashima, T. / Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Ohara, O. / Nagase, T. / Kikuno, R. / Nakayama, M. / Yokoyama, S.
History
DepositionJun 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4Dec 27, 2023Group: 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: Synaptotagmin IV


Theoretical massNumber of molelcules
Total (without water)15,5201
Polymers15,5201
Non-polymers00
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Synaptotagmin IV / / KIAA1342


Mass: 15519.801 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: Kazusa cDNA fj00418 / Plasmid: P020924-36 / References: UniProt: Q9H2B2

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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: 0.75mM 13C, 15N-labeled protein; 20mM Tris-d11; 100mM NaCl; 1mM DTT; 0.1mM NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.822Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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