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- PDB-2lpf: R state structure of monomeric phospholamban (C36A, C41F, C46A) -

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Basic information

Entry
Database: PDB / ID: 2lpf
TitleR state structure of monomeric phospholamban (C36A, C41F, C46A)
ComponentsCardiac phospholamban
KeywordsMEMBRANE PROTEIN / phospholamban / excited state / dilated cardiomyopathy
Function / homology
Function and homology information


negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of relaxation of muscle / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / negative regulation of calcium ion transmembrane transporter activity / acrosome assembly / negative regulation of calcium ion import ...negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of relaxation of muscle / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / negative regulation of calcium ion transmembrane transporter activity / acrosome assembly / negative regulation of calcium ion import / negative regulation of catalytic activity / ATPase inhibitor activity / cardiac muscle tissue development / regulation of cardiac muscle cell contraction / enzyme inhibitor activity / negative regulation of heart rate / muscle cell cellular homeostasis / 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 / 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 / Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cardiac phospholamban
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / molecular dynamics
Model detailsmedian structure, model 1
AuthorsDe Simone, A. / Montalvao, R.W. / Gustavsson, M. / Shi, L. / Veglia, G. / Vendruscolo, M.
CitationJournal: Biochemistry / Year: 2013
Title: Structures of the Excited States of Phospholamban and Shifts in Their Populations upon Phosphorylation.
Authors: De Simone, A. / Gustavsson, M. / Montalvao, R.W. / Shi, L. / Veglia, G. / Vendruscolo, M.
History
DepositionFeb 11, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
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 / 16000median structure
RepresentativeModel #1median structure

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Components

#1: Protein Cardiac phospholamban / PLB


Mass: 6150.477 Da / Num. of mol.: 1 / Mutation: C36A, C41F, C46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PLN / Production host: Escherichia coli (E. coli) / References: UniProt: P61015

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1223D HNCO
1313D C(CO)NH
1412D 1H-15N HSQC
1522D 1H-15N HSQC
1632D 1H-15N HSQC
1712D HN(a/b-NCO-J)-TROSY
1822D HN(a/b-NC0-J)-TROSY
1913D C(CO)NH
11013D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11-1.5 mM [U-99% 13C; U-99% 15N] Phospholamban, 120 mM sodium chloride, 5 % D2O, 20 mM sodium phosphate, 100 mM dodecylphosphocholine, 95% H2O/5% D2O95% H2O/5% D2O
21-1.5 mM [U-99% 13C; U-99% 15N] Phospholamban, 120 mM sodium chloride, 5 % D2O, 20 mM sodium phosphate, 100 mM dodecylphosphocholine, 5.1 % acrylamide, 1.3 % bis-acrylamide, 95% H2O/5% D2O95% H2O/5% D2O
31-1.5 mM [U-99% 13C; U-99% 15N] Phospholamban, 120 mM sodium chloride, 5 % D2O, 20 mM sodium phosphate, 100 mM dodecylphosphocholine, 3.85 % acrylamide, 1.3 % bis-acrylamide, 1.25 % 2-(acrylamido)-2-methyl-1-propanesulfonic acid, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMPhospholamban-1[U-99% 13C; U-99% 15N]1-1.51
120 mMsodium chloride-21
5 %D2O-31
20 mMsodium phosphate-41
100 mMdodecylphosphocholine-51
mMPhospholamban-6[U-99% 13C; U-99% 15N]1-1.52
120 mMsodium chloride-72
5 %D2O-82
20 mMsodium phosphate-92
100 mMdodecylphosphocholine-102
5.1 %acrylamide-112
1.3 %bis-acrylamide-122
mMPhospholamban-13[U-99% 13C; U-99% 15N]1-1.53
120 mMsodium chloride-143
5 %D2O-153
20 mMsodium phosphate-163
100 mMdodecylphosphocholine-173
3.85 %acrylamide-183
1.3 %bis-acrylamide-193
1.25 %2-(acrylamido)-2-methyl-1-propanesulfonic acid-203
Sample conditionsIonic strength: 0.120 / pH: 6.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
GROMACSBerendsens et. al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Restrained molecular dynamics simulations implementing RDC
NMR representativeSelection criteria: median structure
NMR ensembleConformer selection criteria: median structure / Conformers calculated total number: 16000 / Conformers submitted total number: 1

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