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- PDB-2kyv: Hybrid solution and solid-state NMR structure ensemble of phospho... -

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Basic information

Entry
Database: PDB / ID: 2kyv
TitleHybrid solution and solid-state NMR structure ensemble of phospholamban pentamer
ComponentsPhospholamban
KeywordsMEMBRANE PROTEIN / phospholamban / solid state NMR / hybrid method
Function / homology
Function and homology information


: / circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / phospholamban complex / 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 / negative regulation of calcium ion import ...: / circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / phospholamban complex / 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 / negative regulation of calcium ion import / acrosome assembly / ATPase inhibitor activity / regulation of cardiac muscle cell contraction / cardiac muscle tissue development / regulation of cardiac muscle contraction by calcium ion signaling / negative regulation of heart rate / muscle cell cellular homeostasis / locomotor rhythm / regulation of calcium ion transport / enzyme inhibitor activity / 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 speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SOLID-STATE NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsVerardi, R. / Shi, L. / Traaseth, N.J. / Veglia, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method.
Authors: Verardi, R. / Shi, L. / Traaseth, N.J. / Walsh, N. / Veglia, G.
History
DepositionJun 8, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholamban
B: Phospholamban
C: Phospholamban
D: Phospholamban
E: Phospholamban


Theoretical massNumber of molelcules
Total (without water)30,4975
Polymers30,4975
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)20 / 200structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein
Phospholamban


Mass: 6099.499 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pln / Production host: Escherichia coli (E. coli) / References: UniProt: P61015*PLUS

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1312D 1H-13C HSQC
242PISEMA
252SAMPI4

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM beta-mercaptoethanol-1, 5 % D2O-2, 0.02 % sodium azide-3, 300 mM DPC-4, 20 mM sodium phosphate-5, 120 mM sodium chloride-6, 95% H2O/5% D2O95% H2O/5% D2O
240 uM DOPC-7, 11 uM DOPE-8, 5 mM DTT-9, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMbeta-mercaptoethanol-11
5 %D2O-21
0.02 %sodium azide-31
300 mMDPC-41
20 mMsodium phosphate-51
120 mMsodium chloride-61
40 uMDOPC-72
11 uMDOPE-82
5 mMDTT-92
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11506ambient 310 K
2278 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS6001
Bruker ARXBrukerARX6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2155 / NOE intraresidue total count: 639 / NOE long range total count: 85 / NOE medium range total count: 656 / NOE sequential total count: 775 / Protein chi angle constraints total count: 127 / Protein other angle constraints total count: 65 / Protein phi angle constraints total count: 140 / Protein psi angle constraints total count: 145
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.5 Å / Maximum torsion angle constraint violation: 0.7 ° / Maximum upper distance constraint violation: 0.5 Å / Torsion angle constraint violation method: xplor-nih
NMR ensemble rmsDistance rms dev: 0.05 Å / Distance rms dev error: 0.003 Å

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