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- PDB-2adz: solution structure of the joined PH domain of alpha1-syntrophin -

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Basic information

Entry
Database: PDB / ID: 2adz
Titlesolution structure of the joined PH domain of alpha1-syntrophin
ComponentsAlpha-1-syntrophin
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


regulation of vasoconstriction by circulating norepinephrine / negative regulation of peptidyl-cysteine S-nitrosylation / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transport / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / anchoring junction / neuromuscular junction development / nitric-oxide synthase binding / sodium channel regulator activity ...regulation of vasoconstriction by circulating norepinephrine / negative regulation of peptidyl-cysteine S-nitrosylation / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transport / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / anchoring junction / neuromuscular junction development / nitric-oxide synthase binding / sodium channel regulator activity / regulation of heart rate / PDZ domain binding / neuromuscular junction / sarcolemma / actin binding / ATPase binding / postsynaptic membrane / transmembrane transporter binding / cytoskeleton / calmodulin binding / structural molecule activity / protein-containing complex / cytoplasm
Similarity search - Function
Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / Syntrophin C-terminal PH domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / PDZ domain / Pleckstrin homology domain. ...Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / Syntrophin C-terminal PH domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsYan, J. / Wen, W. / Xu, W. / Long, J.F. / Adams, M.E. / Froehner, S.C. / Zhang, M.
CitationJournal: Embo J. / Year: 2005
Title: Structure of the split PH domain and distinct lipid-binding properties of the PH-PDZ supramodule of alpha-syntrophin
Authors: Yan, J. / Wen, W. / Xu, W. / Long, J.F. / Adams, M.E. / Froehner, S.C. / Zhang, M.
History
DepositionJul 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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: Alpha-1-syntrophin


Theoretical massNumber of molelcules
Total (without water)18,6361
Polymers18,6361
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Alpha-1-syntrophin / alpha-syntrophin


Mass: 18635.727 Da / Num. of mol.: 1 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET32a(a modified version) / Production host: Escherichia coli (E. coli) / References: UniProt: Q61234

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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
1332D NOESY
1432D TOCSY
152(H)CCH TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM protein 15N; 100mM potassium phosphate pH 7.090% H2O/10% D2O
21mM protein 15N, 13C; 100mM potassium phosphate pH 7.099.9% D2O
31mM unlabelled protein; 100mM potassium phosphate pH 7.099.9% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1940 restraints, 1776 are NOE-derived distance constraints, 84 dihedral angle restraints,80 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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