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- PDB-2a20: Solution structure of Rim2 Zinc Finger Domain -

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Basic information

Entry
Database: PDB / ID: 2a20
TitleSolution structure of Rim2 Zinc Finger Domain
ComponentsRegulating synaptic membrane exocytosis protein 2
KeywordsMETAL BINDING PROTEIN / Zinc-finger Domain
Function / homology
Function and homology information


regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / maintenance of presynaptic active zone structure / cytoskeleton of presynaptic active zone / spontaneous neurotransmitter secretion / synaptic vesicle docking / inhibitory synapse / calcium ion-regulated exocytosis of neurotransmitter / presynaptic active zone cytoplasmic component / photoreceptor ribbon synapse ...regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / maintenance of presynaptic active zone structure / cytoskeleton of presynaptic active zone / spontaneous neurotransmitter secretion / synaptic vesicle docking / inhibitory synapse / calcium ion-regulated exocytosis of neurotransmitter / presynaptic active zone cytoplasmic component / photoreceptor ribbon synapse / calcium-ion regulated exocytosis / positive regulation of dendrite extension / regulation of exocytosis / positive regulation of inhibitory postsynaptic potential / neurotransmitter secretion / insulin secretion / synaptic vesicle priming / regulation of synaptic vesicle exocytosis / exocytosis / positive regulation of excitatory postsynaptic potential / GABA-ergic synapse / positive regulation of synaptic transmission / cell projection / establishment of localization in cell / regulation of membrane potential / intracellular protein transport / regulation of synaptic plasticity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / small GTPase binding / protein-macromolecule adaptor activity / presynaptic membrane / transmembrane transporter binding / cell differentiation / protein domain specific binding / glutamatergic synapse / positive regulation of gene expression / protein-containing complex binding / protein-containing complex / metal ion binding
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #120 / Rim-like / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / C2 domain ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #120 / Rim-like / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulating synaptic membrane exocytosis protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDulubova, I. / Lou, X. / Lu, J. / Huryeva, I. / Alam, A. / Schneggenburger, R. / Sudhof, T.C. / Rizo, J.
CitationJournal: Embo J. / Year: 2005
Title: A Munc13/RIM/Rab3 tripartite complex: from priming to plasticity?
Authors: Dulubova, I. / Lou, X. / Lu, J. / Huryeva, I. / Alam, A. / Schneggenburger, R. / Sudhof, T.C. / Rizo, J.
History
DepositionJun 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: Regulating synaptic membrane exocytosis protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0023
Polymers6,8711
Non-polymers1312
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6870.929 Da / Num. of mol.: 1 / Fragment: Zinc-finger domain, FYVE-Type, residues 83-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rims2, Rim2 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9JIS1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1332D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N,13C Rim2 ZF domain, 20 mM Pipes pH 6.9, 150 mM NaCl, 1 mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM U-15N Rim2 ZF domain, 20 mM Pipes pH 6.9, 150 mM NaCl, 1 mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
31mM U-15N Rim2 ZF domain, 20 mM Pipes pH 6.9, 150 mM NaCl, 1 mM TCEP, 100% D2O100% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 6.9 / Pressure: ambient / Temperature: 298 K

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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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionClassification
NMRPipe2.3processing
NMRView5.0.16data analysis
ARIA2.0astructure solution
CNS1.1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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