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- PDB-2kb7: Hybrid solution and solid-state NMR structure of monomeric phosph... -

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Basic information

Entry
Database: PDB / ID: 2kb7
TitleHybrid solution and solid-state NMR structure of monomeric phospholamban in lipid bilayers
ComponentsPhospholamban
KeywordsMEMBRANE PROTEIN / phospholamban / PISEMA / hybrid method / lipid bilayers / topology
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 / 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 speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SOLID-STATE NMR / simulated annealing
AuthorsTraaseth, N.J. / Shi, L. / Verardi, R. / Veglia, G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure and topology of monomeric phospholamban in lipid membranes determined by a hybrid solution and solid-state NMR approach.
Authors: Traaseth, N.J. / Shi, L. / Verardi, R. / Mullen, D.G. / Barany, G. / Veglia, G.
#1: Journal: J.Biomol.Nmr / Year: 2009
Title: A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints.
Authors: Shi, L. / Traaseth, N.J. / Verardi, R. / Cembran, A. / Gao, J. / Veglia, G.
History
DepositionNov 21, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 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
P: 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)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Phospholamban /


Mass: 6150.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Bl21de3phi / Gene: pln / Plasmid: pMAL / 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 H(CCO)NH
1313D C(CO)NH
1413D 1H-15N NOESY
2522D [1H,15N] PISEMA
2622D [1H,15N]SAMPI4

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 15N] and [U-99% 13C; U-99% 15N] Phospholamban, 90% H2O/10% D2O90% H2O/10% D2O
2160/1 lipid/protein (mol/mol) [U-99% 15N] and [15N-Ala] and [15N-Arg] and [15N-Asn] and [15N-Ile] and [15N-Met] and [15N-Leu] and [15N-Phe] and [15N-Val] and [15N-Ser] and [15N-Gln26,Gln29] Phospholamban, 100% H2O100% H2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingSolution-ID
1.5 mMPhospholamban[U-99% 15N] and [U-99% 13C; U-99% 15N]1
%Phospholamban[U-99% 15N] and [15N-Ala] and [15N-Arg] and [15N-Asn] and [15N-Ile] and [15N-Met] and [15N-Leu] and [15N-Phe] and [15N-Val] and [15N-Ser] and [15N-Gln26,Gln29]2
Sample conditionspH: 6.0 / Pressure: ambient / Temperature units: K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Varian VNMRSVarianVNMRS7002
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18Schwieters, C. et al.refinement
X-PLOR NIH2.18Schwieters, C. et al.data analysis
X-PLOR NIH2.18Schwieters, C. et al.structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Authors state that they define the z-axis to be parallel with the bilayer normal. Also, the origin (or in other words, when the z Cartesian coordinate is 0) is defined to be the center of the lipid bilayer.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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