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- PDB-1jzp: Modified Peptide A (D18-A1) of the Rabbit Skeletal Dihydropyridin... -

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Basic information

Entry
Database: PDB / ID: 1jzp
TitleModified Peptide A (D18-A1) of the Rabbit Skeletal Dihydropyridine Receptor
ComponentsSkeletal Dihydropydrine Receptor
KeywordsSIGNALING PROTEIN / Alpha helical peptide / DHPR / D-isomer
Function / homology
Function and homology information


positive regulation of muscle contraction / L-type voltage-gated calcium channel complex / cellular response to caffeine / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / T-tubule / muscle contraction / calcium ion transmembrane transport / transmembrane transporter binding ...positive regulation of muscle contraction / L-type voltage-gated calcium channel complex / cellular response to caffeine / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / T-tubule / muscle contraction / calcium ion transmembrane transport / transmembrane transporter binding / calmodulin binding / metal ion binding / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, L-type, alpha-1S subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated ...Voltage-dependent calcium channel, L-type, alpha-1S subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit alpha-1S
Similarity search - Component
MethodSOLUTION NMR / Distance Geometry Simulated annealing refinement
AuthorsGreen, D. / Pace, S. / Sakowska, M. / Dulhunty, A.F. / Casarotto, M.G.
CitationJournal: Biochem.J. / Year: 2003
Title: The three-dimensional structural surface of two beta-sheet scorpion toxins mimics that of an alpha-helical dihydropyridine receptor segment.
Authors: Green, D. / Pace, S. / Curtis, S.M. / Sakowska, M. / Lamb, G.D. / Dulhunty, A.F. / Casarotto, M.G.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Skeletal Dihydropydrine Receptor


Theoretical massNumber of molelcules
Total (without water)2,3381
Polymers2,3381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 17
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Skeletal Dihydropydrine Receptor


Mass: 2337.772 Da / Num. of mol.: 1 / Fragment: D18-A1 / Mutation: Arg688 from L to D isomer / Source method: obtained synthetically
Details: This sequence is a modification of a segment of a protein that occurs naturally in rabbit skeletal muscle.
References: UniProt: P07293*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
NMR detailsText: This structure was determined by using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2-3 mM DHPR peptide, unbuffered / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.0 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.851 / Developer: Brunger / Classification: refinement
RefinementMethod: Distance Geometry Simulated annealing refinement / Software ordinal: 1
Details: The structure is based on a total of 239 restraints of which 222 are NOE-derived, 12 are dihedral angle restraints and 5 are distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers calculated total number: 17 / Conformers submitted total number: 1

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