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- PDB-1n7l: Solution NMR structure of phospholamban in detergent micelles -

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Basic information

Entry
Database: PDB / ID: 1n7l
TitleSolution NMR structure of phospholamban in detergent micelles
ComponentsCardiac phospholamban
KeywordsSIGNALING PROTEIN / helix-turn-helix
Function / homology
Function and homology information


negative regulation of calcium ion binding / circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / acrosome assembly / negative regulation of calcium ion transmembrane transporter activity ...negative regulation of calcium ion binding / circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / acrosome assembly / negative regulation of calcium ion transmembrane transporter activity / negative regulation of catalytic activity / negative regulation of calcium ion import / ATPase inhibitor activity / regulation of cardiac muscle cell contraction / cardiac muscle tissue development / negative regulation of heart rate / muscle cell cellular homeostasis / locomotor rhythm / enzyme inhibitor activity / regulation of calcium ion transport / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Notch signaling pathway / sarcoplasmic reticulum membrane / mitochondrial membrane / visual learning / intracellular calcium ion homeostasis / ATPase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / identical protein binding
Similarity search - Function
Phospholamban / Phospholamban / Phospholamban / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / simulated annealing
AuthorsZamoon, J. / Mascioni, A. / Thomas, D.D. / Veglia, G.
CitationJournal: Biophys.J. / Year: 2003
Title: NMR solution structure and topological orientation of monomeric phospholamban in dodecylphosphocholine micelles.
Authors: Zamoon, J. / Mascioni, A. / Thomas, D.D. / Veglia, G.
History
DepositionNov 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: Cardiac phospholamban


Theoretical massNumber of molelcules
Total (without water)6,1501
Polymers6,1501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #15fewest violations

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Components

#1: Protein Cardiac phospholamban / PLB


Mass: 6150.477 Da / Num. of mol.: 1 / Mutation: C37A C42F C47A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PLN / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3phi / References: UniProt: P61015

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
131HNCA
141HN(CO)CA
151HN(CA)CB
161HNCO

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Sample preparation

DetailsContents: 1 mM phospholamban U-15N,13C; 20 mM phosphate buffer; 90% H2O, 10% D2O; pH=4.2; 600 mM DPC;
Sample conditionspH: 4.2 / 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
NMRPipeFrank Delaglioprocessing
NMRView5Bruce A. Johnsondata analysis
XPLOR-NIH2.0.4G. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandrastructure solution
XPLOR-NIH2.0.4Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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