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- PDB-2m3b: Serine 16 phosphorylated phospholamban pentamer, Hybrid solution ... -

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Basic information

Entry
Database: PDB / ID: 2m3b
TitleSerine 16 phosphorylated phospholamban pentamer, Hybrid solution and solid-state NMR structural ensemble
ComponentsCardiac phospholamban
KeywordsMEMBRANE PROTEIN / phospholamban / pln / plb
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 speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / SOLID-STATE NMR / simulated annealing
Model detailslowest energy, model1
AuthorsVostrikov, V.V. / Verardi, R. / Veglia, G.
CitationJournal: Structure / Year: 2013
Title: Structural Dynamics and Topology of Phosphorylated Phospholamban Homopentamer Reveal Its Role in the Regulation of Calcium Transport.
Authors: Vostrikov, V.V. / Mote, K.R. / Verardi, R. / Veglia, G.
History
DepositionJan 15, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn
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_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)30,8975
Polymers30,8975
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein
Cardiac phospholamban / PLB


Mass: 6179.478 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PLN / Plasmid: pMAL-c2X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61015

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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
1323D 1H-15N NOESY
3432D PISEMA
2542D DARR

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1 mM [U-100% 13C; U-100% 15N] phospholamban, 300 mM [U-2H] DPC, 20 mM sodium phosphate, 120 mM sodium chloride, 10 mM beta-mercaptoethanol, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.15 mM [U-13C; U-15N; U-2H] phospholamban, 300 mM DPC, 20 mM sodium phosphate, 120 mM sodium chloride, 10 mM beta-mercaptoethanol, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
34 mg [U-100% 15N] phospholamban, 38 mg DOPC, 9 mg DOPE, 100% H2O100% H2O
41 mg [U-100% 13C; U-100% 15N] phospholamban, 12 mg DOPC, 3 mg DOPE, 20 mM MOPS, 50 mM sodium chloride, 0.02 % sodium azide, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMphospholamban-1[U-100% 13C; U-100% 15N]1
300 mMDPC-2[U-2H]1
20 mMsodium phosphate-31
120 mMsodium chloride-41
10 mMbeta-mercaptoethanol-51
0.02 %sodium azide-61
0.15 mMphospholamban-7[U-13C; U-15N; U-2H]2
300 mMDPC-82
20 mMsodium phosphate-92
120 mMsodium chloride-102
10 mMbeta-mercaptoethanol-112
0.02 %sodium azide-122
4 mMphospholamban-13[U-100% 15N]3
38 mMDOPC-143
9 mMDOPE-153
1 mMphospholamban-16[U-100% 13C; U-100% 15N]4
12 mMDOPC-174
3 mMDOPE-184
20 mMMOPS-194
50 mMsodium chloride-204
0.02 %sodium azide-214
Sample conditions
Conditions-IDpHTemperature (K)
16 310 K
27 258 K
37 298 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7002
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe7.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.114Goddarddata analysis
MolProbityDavid C. Richardsondata analysis
PSVSBhattacharya and Montelionedata analysis
X-PLOR NIH2.33Schwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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