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- PDB-2fn5: NMR Structure of the Neurabin PDZ domain (502-594) -

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Basic information

Entry
Database: PDB / ID: 2fn5
TitleNMR Structure of the Neurabin PDZ domain (502-594)
ComponentsNeurabin-1
KeywordsSIGNALING PROTEIN / PDZ / Neurabin
Function / homology
Function and homology information


growth cone lamellipodium / negative regulation of spontaneous neurotransmitter secretion / regulation of synapse structural plasticity / positive regulation of long-term synaptic depression / cellular response to toxic substance / postsynaptic actin cytoskeleton organization / postsynaptic actin cytoskeleton / protein phosphatase 1 binding / regulation of filopodium assembly / regulation of actin filament polymerization ...growth cone lamellipodium / negative regulation of spontaneous neurotransmitter secretion / regulation of synapse structural plasticity / positive regulation of long-term synaptic depression / cellular response to toxic substance / postsynaptic actin cytoskeleton organization / postsynaptic actin cytoskeleton / protein phosphatase 1 binding / regulation of filopodium assembly / regulation of actin filament polymerization / regulation of dendritic spine morphogenesis / negative regulation of stress fiber assembly / regulation of synapse assembly / cortical actin cytoskeleton / positive regulation of dendritic spine development / dendritic spine neck / negative regulation of long-term synaptic potentiation / neuron development / excitatory postsynaptic potential / filopodium / calcium-mediated signaling / actin filament organization / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of neuron projection development / neuron projection development / actin filament binding / actin cytoskeleton / GTPase binding / lamellipodium / growth cone / transmembrane transporter binding / dendritic spine / postsynaptic density / cytoskeleton / protein domain specific binding / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / protein kinase binding / identical protein binding / cytoplasm
Similarity search - Function
Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / PDZ domain / Pdz3 Domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / PDZ domain / Pdz3 Domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsDancheck, B. / Peti, W.
CitationJournal: Biochemistry / Year: 2007
Title: Structural basis for spinophilin-neurabin receptor interaction.
Authors: Kelker, M.S. / Dancheck, B. / Ju, T. / Kessler, R.P. / Hudak, J. / Nairn, A.C. / Peti, W.
History
DepositionJan 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurabin-1


Theoretical massNumber of molelcules
Total (without water)9,9481
Polymers9,9481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Neurabin-1 / Neurabin-I / Neural tissue-specific F-actin binding protein I / Protein phosphatase 1 regulatory ...Neurabin-I / Neural tissue-specific F-actin binding protein I / Protein phosphatase 1 regulatory subunit 9A / p180 / PP1bp175


Mass: 9948.273 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1r9a / Plasmid: RP1B / Species (production host): Escherichia coli / Cell line (production host): IRL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O35867

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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
1312D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
13.5 mM Neurabin PDZ 502-594 U-15N,13C, 20 mM Naphosphate buffer pH 6.5, 50 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
23.5 mM Neurabin PDZ 502-594 U-15N, 20 mM Naphosphate buffer pH 6.5, 50 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.5 / 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
Bruker DRXBrukerDRX6001
Bruker AVANCE IIBrukerAVANCE II5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Brukercollection
TopSpin1.3Brukerprocessing
CARA1.3www.nmr.chdata analysis
ATNOS/CANDID1Torsten Herrmannstructure solution
CYANA2Peter Guentertstructure solution
CNS1.2Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water shell using RECOORD skripts
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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