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- PDB-1du1: PEPTIDE FRAGMENT THR671-LEU690 OF THE RABBIT SKELETAL DIHYDROPYRI... -

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Basic information

Entry
Database: PDB / ID: 1du1
TitlePEPTIDE FRAGMENT THR671-LEU690 OF THE RABBIT SKELETAL DIHYDROPYRIDINE RECEPTOR
ComponentsSKELETAL DIHYDROPYRIDINE RECEPTOR
KeywordsSIGNALING PROTEIN / DIHYDROPYRIDINE RECEPTOR / RYANODINE RECEPTOR
Function / homology
Function and homology information


positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / cellular response to caffeine / calcium ion import across plasma membrane / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / T-tubule / muscle contraction ...positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / cellular response to caffeine / calcium ion import across plasma membrane / 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 / simulated annealing
AuthorsCasarotto, M. / Dulhunty, A.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: A structural requirement for activation of skeletal ryanodine receptors by peptides of the dihydropyridine receptor II-III loop.
Authors: Casarotto, M.G. / Gibson, F. / Pace, S.M. / Curtis, S.M. / Mulcair, M. / Dulhunty, A.F.
#1: Journal: Biophys.J. / Year: 1999
Title: Activation and inhibition of skeletal RyR channels by a part of the skeletal DHPR II-III loop: effects of DHPR Ser687 and FKBP12
Authors: Dulhunty, A.F. / Laver, D.R. / Gallant, E.M. / Casarotto, M.G. / Pace, S.M. / Curtis, S. / Pace, S. / Curtis, S. / Mulcair, M.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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 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: SKELETAL DIHYDROPYRIDINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)2,3401
Polymers2,3401
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)1 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide SKELETAL DIHYDROPYRIDINE RECEPTOR


Mass: 2339.764 Da / Num. of mol.: 1 / Fragment: II-III LOOP REGION, FRAGMENT THR671-LEU690 A1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide naturally occurs in rabbit (Oryctolagus cuniculus)
References: UniProt: P07293

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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 deternined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 4 mM peptide, no buffer / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 5.0 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 223 restraints, 212 are NOE-derived distance constraints, 7 dihedral angle restraints and 4 distance constraints derived from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 1

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