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- PDB-1zub: Solution Structure of the RIM1alpha PDZ Domain in Complex with an... -

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Basic information

Entry
Database: PDB / ID: 1zub
TitleSolution Structure of the RIM1alpha PDZ Domain in Complex with an ELKS1b C-terminal Peptide
Components
  • ELKS1b
  • Regulating synaptic membrane exocytosis protein 1
KeywordsENDOCYTOSIS/EXOCYTOSIS / PDZ domain / complex / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


positive regulation of synaptic vesicle priming / positive regulation of synaptic vesicle fusion to presynaptic active zone membrane / extrinsic component of presynaptic active zone membrane / acrosomal vesicle exocytosis / 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 / IkappaB kinase complex / spontaneous neurotransmitter secretion ...positive regulation of synaptic vesicle priming / positive regulation of synaptic vesicle fusion to presynaptic active zone membrane / extrinsic component of presynaptic active zone membrane / acrosomal vesicle exocytosis / 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 / IkappaB kinase complex / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / calcium ion-regulated exocytosis of neurotransmitter / inhibitory synapse / neuromuscular synaptic transmission / regulation of presynaptic cytosolic calcium ion concentration / presynaptic active zone cytoplasmic component / positive regulation of dendrite extension / positive regulation of inhibitory postsynaptic potential / neurotransmitter secretion / retrograde transport, endosome to Golgi / presynaptic cytosol / podosome / regulation of synaptic vesicle exocytosis / synaptic vesicle priming / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission / GABA-ergic synapse / regulation of membrane potential / ciliary basal body / cell projection / PDZ domain binding / long-term synaptic potentiation / intracellular protein transport / regulation of long-term neuronal synaptic plasticity / regulation of synaptic plasticity / small GTPase binding / SH3 domain binding / protein transport / synaptic vesicle / presynaptic membrane / protein-containing complex assembly / vesicle / transmembrane transporter binding / postsynaptic density / cell differentiation / Golgi membrane / centrosome / glutamatergic synapse / synapse / regulation of DNA-templated transcription / positive regulation of gene expression / protein kinase binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Active zone protein ELKS / RIM-binding protein of the cytomatrix active zone / Rim-like / : / RIM2-alpha zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Protein kinase C conserved region 2 (CalB) ...Active zone protein ELKS / RIM-binding protein of the cytomatrix active zone / Rim-like / : / RIM2-alpha zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / PDZ domain / C2 domain / C2 domain profile. / Pdz3 Domain / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
ELKS/Rab6-interacting/CAST family member 1 / Regulating synaptic membrane exocytosis protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLu, J. / Li, H. / Wang, Y. / Sudhof, T.C. / Rizo, J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Solution Structure of the RIM1alpha PDZ Domain in Complex with an ELKS1b C-terminal Peptide
Authors: Lu, J. / Li, H. / Wang, Y. / Sudhof, T.C. / Rizo, J.
History
DepositionMay 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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 1
B: ELKS1b


Theoretical massNumber of molelcules
Total (without water)13,5382
Polymers13,5382
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 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 12244.122 Da / Num. of mol.: 1 / Fragment: PDZ Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rims1, Rim1 / Plasmid: pGEX-KT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codon+ / References: UniProt: Q9JIR4
#2: Protein/peptide ELKS1b / ERC protein 1 / ERC1 / CAZ-associated structural protein 2 / CAST2 / RAB6 interacting protein 2 / C- ...ERC protein 1 / ERC1 / CAZ-associated structural protein 2 / CAST2 / RAB6 interacting protein 2 / C-terminal peptide


Mass: 1294.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rab6ip2, Cast2, Elks, Erc1 / Plasmid: pTMHa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q811U3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1343D 15N-separated NOESY
1453D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM Rim1alpha PDZ domain U-15N, 0.75mM ELKS1b C-terminal peptide, 20mM Mes buffer, 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM Rim1alpha PDZ domain U-15N, 13C, 0.75mM ELKS1b C-terminal peptide, 20mM Mes buffer, 90% H2O, 10% D2O90% H2O/10% D2O
30.5mM Rim1alpha PDZ domain U-15N,10%-13C, 0.75mM ELKS1b C-terminal peptide, 20mM Mes buffer, 90% H2O, 10% D2O90% H2O/10% D2O
40.5mM ELKS1b C-terminal peptide U-15N, 0.75mM Rim1alpha PDZ domain, 20mM Mes buffer, 90% H2O, 10% D2O90% H2O/10% D2O
50.5mM ELKS1b C-terminal peptide U-15N, 13C, 0.75mM Rim1alpha PDZ domain, 20mM Mes buffer, 90% H2O, 10% D2O90% H2O/10% D2O
60.5mM ELKS1b C-terminal peptide U-15N, 10%-13C, 0.75mM Rim1alpha PDZ domain, 20mM Mes buffer, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 303 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
NameVersionDeveloperClassification
CNS1.1Brungerrefinement
NMRPipe2.3Delaglioprocessing
NMRView5.1Johnsondata analysis
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: 1000 / Conformers submitted total number: 20

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