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- PDB-2pdz: SOLUTION STRUCTURE OF THE SYNTROPHIN PDZ DOMAIN IN COMPLEX WITH T... -

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Basic information

Entry
Database: PDB / ID: 2pdz
TitleSOLUTION STRUCTURE OF THE SYNTROPHIN PDZ DOMAIN IN COMPLEX WITH THE PEPTIDE GVKESLV, NMR, 15 STRUCTURES
Components
  • PEPTIDE GVKESLV
  • SYNTROPHIN
KeywordsCOMPLEX (SYNTROPHIN/PEPTIDE) / SYNTROPHIN PDZ DOMAIN / VOLTAGE-GATED SODIUM CHANNEL / COMPLEX (SYNTROPHIN-PEPTIDE) / COMPLEX (SYNTROPHIN-PEPTIDE) complex
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 / PDZ domain / Pdz3 Domain / PH domain / PH domain profile. / PDZ domain / Pleckstrin homology domain. ...Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / Syntrophin C-terminal PH domain / PDZ domain / Pdz3 Domain / 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
AuthorsSchultz, J. / Hoffmueller, U. / Ashurst, J. / Krause, G. / Schmieder, P. / Macias, M. / Schneider-Mergener, J. / Oschkinat, H.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Specific interactions between the syntrophin PDZ domain and voltage-gated sodium channels.
Authors: Schultz, J. / Hoffmuller, U. / Krause, G. / Ashurst, J. / Macias, M.J. / Schmieder, P. / Schneider-Mergener, J. / Oschkinat, H.
History
DepositionDec 10, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_exptl_sample_conditions.pressure_units
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: SYNTROPHIN
B: PEPTIDE GVKESLV


Theoretical massNumber of molelcules
Total (without water)9,8312
Polymers9,8312
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)15 / 200LOWEST ENERGIES
RepresentativeModel #1

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Components

#1: Protein SYNTROPHIN


Mass: 9255.769 Da / Num. of mol.: 1 / Fragment: PDZ DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Organ: HEART / Plasmid: PET 21D / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Organ (production host): HEART / Production host: Escherichia coli (E. coli) / Strain (production host): PET / Tissue (production host): MUSCLE / References: UniProt: Q61234
#2: Protein/peptide PEPTIDE GVKESLV


Mass: 575.675 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 2-PEPTIDE FROM C-TERMINUS OF ALPHA-SUBUNIT OF VOLTAGE-GATED SODIUM CHANNELS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
1212D-TOCSY
1311H-15 NOESY AND TOCSY
1411H-13C NOESY
151(H)CCH-TOCSY
161(H)CCH-COSY
171CBCANH
181CBCA(CO)NH
191HNCA
1101HN(CO)CA
11111H-13C HQQC-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED SYNTROPHIN PDZ DOMAIN

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 70mM / pH: 6.2 / Pressure: 1 atm / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX600BrukerDRX6006001
Bruker DRX750BrukerDRX7507502

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGIES / Conformers calculated total number: 200 / Conformers submitted total number: 15

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