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- PDB-1jdm: NMR Structure of Sarcolipin -

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Basic information

Entry
Database: PDB / ID: 1jdm
TitleNMR Structure of Sarcolipin
ComponentsSarcolipin
KeywordsMEMBRANE PROTEIN / Helix
Function / homology
Function and homology information


positive regulation of protein depolymerization / regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of relaxation of muscle / negative regulation of calcium ion transmembrane transporter activity / negative regulation of protein-containing complex disassembly / negative regulation of calcium ion import / negative regulation of catalytic activity / sarcoplasmic reticulum calcium ion transport ...positive regulation of protein depolymerization / regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of relaxation of muscle / negative regulation of calcium ion transmembrane transporter activity / negative regulation of protein-containing complex disassembly / negative regulation of calcium ion import / negative regulation of catalytic activity / sarcoplasmic reticulum calcium ion transport / enzyme inhibitor activity / Ion transport by P-type ATPases / regulation of calcium ion transport / Ion homeostasis / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / calcium ion transport / positive regulation of cold-induced thermogenesis / ATPase binding / membrane
Similarity search - Function
MethodSOLUTION NMR / simulated annealing
AuthorsVeglia, G. / Mascioni, A.
CitationJournal: Biochemistry / Year: 2002
Title: Structure and orientation of sarcolipin in lipid environments.
Authors: Mascioni, A. / Karim, C. / Barany, G. / Thomas, D.D. / Veglia, G.
History
DepositionJun 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 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 / 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: Sarcolipin


Theoretical massNumber of molelcules
Total (without water)3,7641
Polymers3,7641
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)16 / 50structures with the least restraint violations
RepresentativeModel #7closest to the average

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Components

#1: Protein/peptide Sarcolipin


Mass: 3763.559 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans).
References: UniProt: O00631

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY

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Sample preparation

DetailsContents: 0.7 mM Sarcolipin; 20mM phosphate buffer; 600 mM SDS; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate / pH: 4 / Pressure: 1 atm / Temperature: 323 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: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe1.8Delaglioprocessing
Sparky3.98Thomas, J.data analysis
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 16

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