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- PDB-1v27: Solution structure of the first C2 domain of RIM2 -

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Basic information

Entry
Database: PDB / ID: 1v27
TitleSolution structure of the first C2 domain of RIM2
ComponentsRegulating synaptic membrane exocytosis protein 2
KeywordsENDOCYTOSIS/EXOCYTOSIS / C2 / exocytosis / Rab3-interacting molecule / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


cytoskeleton of presynaptic active zone / spontaneous neurotransmitter secretion / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of inhibitory postsynaptic potential / regulation of exocytosis / calcium-ion regulated exocytosis / positive regulation of dendrite extension / insulin secretion / regulation of synaptic vesicle exocytosis / presynaptic active zone ...cytoskeleton of presynaptic active zone / spontaneous neurotransmitter secretion / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of inhibitory postsynaptic potential / regulation of exocytosis / calcium-ion regulated exocytosis / positive regulation of dendrite extension / insulin secretion / regulation of synaptic vesicle exocytosis / presynaptic active zone / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission / regulation of membrane potential / cell projection / intracellular protein transport / regulation of synaptic plasticity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / small GTPase binding / presynaptic membrane / transmembrane transporter binding / cell differentiation / extracellular exosome / metal ion binding
Similarity search - Function
Rim-like / : / RIM2-alpha zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain ...Rim-like / : / RIM2-alpha zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Regulating synaptic membrane exocytosis protein 2
Similarity search - Component
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 RIM2
Authors: Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionOct 7, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2004Provider: 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: Regulating synaptic membrane exocytosis protein 2


Theoretical massNumber of molelcules
Total (without water)16,4521
Polymers16,4521
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Regulating synaptic membrane exocytosis protein 2 / Rab3-interacting molecule 2 / RIM2


Mass: 16451.578 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 KIAA0751 / Plasmid: P020930-02 / References: UniProt: Q9UQ26

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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: 1.1mM 13C/15N-labeled protein; 20mM TRIS-d11, 100mM NaCl, 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / 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
KUJIRA0.861Kobayashi, 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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