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- PDB-1zll: NMR Structure of Unphosphorylated Human Phospholamban Pentamer -

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Basic information

Entry
Database: PDB / ID: 1zll
TitleNMR Structure of Unphosphorylated Human Phospholamban Pentamer
ComponentsCardiac phospholamban
KeywordsMEMBRANE PROTEIN/SIGNALING PROTEIN / pentamer / leu/ile zipper / super coil / channel / MEMBRANE PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of cardiac muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / regulation of cardiac muscle cell membrane potential / negative regulation of calcium ion transmembrane transporter activity ...regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of cardiac muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / regulation of cardiac muscle cell membrane potential / negative regulation of calcium ion transmembrane transporter activity / acrosome assembly / negative regulation of calcium ion import / negative regulation of catalytic activity / ATPase inhibitor activity / regulation of the force of heart contraction / negative regulation of ATP-dependent activity / cardiac muscle tissue development / regulation of cardiac muscle cell contraction / blood circulation / enzyme inhibitor activity / relaxation of cardiac muscle / regulation of heart contraction / negative regulation of heart rate / muscle cell cellular homeostasis / regulation of calcium ion transport / Ion transport by P-type ATPases / negative regulation of calcium ion transport / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Ion homeostasis / Notch signaling pathway / sarcoplasmic reticulum membrane / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum / mitochondrial membrane / intracellular calcium ion homeostasis / ATPase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane
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
Cardiac phospholamban
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Simulated Annealing, Molecular Dynamics
AuthorsOxenoid, K. / Chou, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: The structure of phospholamban pentamer reveals a channel-like architecture in membranes
Authors: Oxenoid, K. / Chou, J.J.
History
DepositionMay 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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
B: Cardiac phospholamban
C: Cardiac phospholamban
D: Cardiac phospholamban
E: Cardiac phospholamban


Theoretical massNumber of molelcules
Total (without water)30,5735
Polymers30,5735
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 / 30structures with the lowest energy
RepresentativeModel #9fewest violations

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Components

#1: Protein
Cardiac phospholamban / PLB


Mass: 6114.576 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLN / Plasmid: pMALc2x / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26678

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TROSY-HNCA, HN(CA)CB, HN(CA)CO
122measurement of 1H-15N, 13C'-13CA, and 13C'-15N RDCs using 3D HNCO based experiments
133H(CCO)NH, C(CO)NH
14315N-edited NOESY, 13C-edited NOESY
15413C-HSQC for methyl stereospecific assignment
165Double 13C-filtered, 15N-edited NOESY
1763D 15N-edited NOESY
1832D spin-echo difference experiments for measuring 3-bond J(NCg) and J(CCg) couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM Phospholamban Pentamer, U-15N, 13C, 85% 2H, 25 mM Sodium Phosphate buffer, 50 mM BME, 200 mM DPC, 95% H2O, 5% D2O95% H2O/5% D2O
20.05 mM Phospholamban Pentamer, U-15N,13C, 85% 2H, 25 mM Sodium Phosphate buffer, 50 mM BME, 200 mM DPC, 4% stretched polyacrylamide gel, 95% H2O, 5% D2O95% H2O/5% D2O
30.2 mM Phospholamban Pentamer, U-15N,13C, 25 mM Sodium Phosphate buffer, 50 mM BME, 200 mM 2H-DPC, 95% H2O, 5% D2O95% H2O/5% D2O
40.2 mM Phospholamban Pentamer, 10% 13C-labeled, 25 mM Sodium Phosphate buffer, 50 mM BME, 200 mM DPC, 95% H2O, 5% D2O95% H2O/5% D2O
50.2 mM Phospholamban Pentamer, 50% U-15N,13C and 50% unlabeled, 25mM Sodium Phosphate buffer, 50 mM BME, 200 mM 2H-DPC, 95% H2O, 5% D2O95% H2O/5% D2O
60.2 mM Phospholamban Pentamer, 50% U-15N, U-2H and 50% unlabeled; 25mM Sodium Phosphate buffer, 50 mM BME, 200 mM 2H-DPC, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 25 mM Sodium Phosphate / pH: 6.0 / Pressure: ambient / Temperature: 303 K

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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
Bruker AVANCEBrukerAVANCE5001
Bruker DMXBrukerDMX6002
Bruker AVANCEBrukerAVANCE7503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglio et al.processing
XPLOR-NIH2.9.9Schwieters et al.refinement
RefinementMethod: Simulated Annealing, Molecular Dynamics / Software ordinal: 1
Details: 1. Monomer structure was determined with simulated annealing protocol that refines all intramonomer NOEs, sidechain J-couplings, and backbone RDCs. 2. Pentamer is calculated with simulated- ...Details: 1. Monomer structure was determined with simulated annealing protocol that refines all intramonomer NOEs, sidechain J-couplings, and backbone RDCs. 2. Pentamer is calculated with simulated-annealing protocol that treats individual monomer backbones as rigid bodies while satisfying all intermonomer NOEs.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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