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- PDB-2hyn: Complete ensemble of NMR structures of unphosphorylated human pho... -

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Basic information

Entry
Database: PDB / ID: 2hyn
TitleComplete ensemble of NMR structures of unphosphorylated human phospholamban pentamer
ComponentsCardiac phospholamban
KeywordsMEMBRANE PROTEIN/SIGNALING PROTEIN / symmetric homo-oligomer / pentamer / protein complex / 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 / Complete SCS search, Energy-minimization
AuthorsPotluri, S. / Yan, A.K. / Chou, J.J. / Donald, B.R. / Bailey-Kellogg, C.
Citation
Journal: Proteins / Year: 2006
Title: Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing.
Authors: Potluri, S. / Yan, A.K. / Chou, J.J. / Donald, B.R. / Bailey-Kellogg, C.
#1: Journal: 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
DepositionAug 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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)184 / 184All calculated structures were submitted. Our method guarantees that the ensemble represents all structures that satisfy the data and have good vdW packing within a user-defined similarity level (chosen as 1 A).
RepresentativeModel #1lowest energy

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Components

#1: Protein
Cardiac phospholamban


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 experimentType: TROSY-HNCA, HN(CA)CB, HN(CA)CO, MEASUREMENT OF 1H-15N, 13C'- 13CA, AND 13C'-15N RDCS USING 3D HNCO BASED EXPERIMENTS, H(CCO)NH, C(CO)NH, 15N-EDITED NOESY, 13C-EDITED NOESY, 13C- HSQC FOR METHYL ...Type: TROSY-HNCA, HN(CA)CB, HN(CA)CO, MEASUREMENT OF 1H-15N, 13C'- 13CA, AND 13C'-15N RDCS USING 3D HNCO BASED EXPERIMENTS, H(CCO)NH, C(CO)NH, 15N-EDITED NOESY, 13C-EDITED NOESY, 13C- HSQC FOR METHYL STEREOSPECIFIC ASSIGNMENT, DOUBLE 13C- FILTERED, 15N-EDITED NOESY, 3D 15N-EDITED NOESY, 2D SPIN-ECHO DIFFERENCE EXPERIMENTS FOR MEASURING 3-BOND J(NCG) AND J(CCG) COUPLINGS

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Sample preparation

DetailsContents: 0.2 MM PHOSPHOLAMBAN PENTAMER, U-15N, 13C, 85% 2H, 25 MM SODIUM PHOSPHATE BUFFER, 50 MM BME, 200 MM DPC, 95% H2O, 5% D2O;0.2 MM PHOSPHOLAMBAN PENTAMER, U-15N, 13C, 85% 2H, 25 MM SODIUM ...Contents: 0.2 MM PHOSPHOLAMBAN PENTAMER, U-15N, 13C, 85% 2H, 25 MM SODIUM PHOSPHATE BUFFER, 50 MM BME, 200 MM DPC, 95% H2O, 5% D2O;0.2 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% D2O;0.2 MM PHOSPHOLAMBAN PENTAMER, U-15N,13C, 25 MM SODIUM PHOSPHATE BUFFER, 50 MM BME, 200 MM 2H-DPC, 95% H2O, 5% D2O;0.2 MM PHOSPHOLAMBAN PENTAMER, 10% 13C-LABELED, 25 MM SODIUM PHOSPHATE BUFFER, 50 MM BME, 200 MM DPC, 95% H2O, 5% D2O;0.2 MM PHOSPHOLAMBAN PENTAMER, 50% U-15N,13C AND 50% UNLABELED, 25MM SODIUM PHOSPHATE BUFFER, 50 MM BME, 200 MM 2H-DPC, 95% H2O, 5% D2O;0.2 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% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 25 mM SODIUM PHOSPHATE / pH: 6.0 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker Adavnce, DMX / Manufacturer: Bruker / Model: Adavnce, DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Complete SCS search0S. Potluri, A.K. Yan, B. R. Donald, C. Bailey-Kelloggprocessing
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang,J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,L.M.Rice, T.Simonson, G.L.Warrenrefinement
RefinementMethod: Complete SCS search, Energy-minimization / Software ordinal: 1
Details: 1. MONOMER STRUCTURE: DETERMINED WITH SIMULATED ANNEALING PROTOCOL THAT REFINES ALL INTRAMONOMER NOES, SIDECHAIN J-COUPLINGS, AND BACKBONE RDCS. 2. PENTAMER STRUCTURE: DETERMINED BY OUR ...Details: 1. MONOMER STRUCTURE: DETERMINED WITH SIMULATED ANNEALING PROTOCOL THAT REFINES ALL INTRAMONOMER NOES, SIDECHAIN J-COUPLINGS, AND BACKBONE RDCS. 2. PENTAMER STRUCTURE: DETERMINED BY OUR COMPLETE SCS APPROACH. TRADITIONAL NMR PROTOCOLS FOR SYMMETRIC HOMO-OLIGOMERS (USED FOR STRUCTURES OF PDB ID 1ZLL) ARE BASED ON SIMULATED ANNEALING TECHNIQUES AND COULD GET TRAPPED IN LOCAL MINIMA. OUR COMPLETE SCS SEARCH APPROACH AVOIDS BIAS AND RETURNS ALL CONSISTENT, WELL-PACKED STRUCTURES TO WITHIN A USER-DEFINED SIMILARITY LEVEL. ENERGY-MINIMIZATION IS USED ONLY AT A LATER STAGE AFTER THE ENSEMBLE OF STRUCTURES THAT SATISFY THE DATA HAVE BEEN IDENTIFIED, HENCE ENSURING THAT NO CONSISTENT WELL-PACKED CONFORMATION IS MISSED.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: All calculated structures were submitted. Our method guarantees that the ensemble represents all structures that satisfy the data and have good vdW packing within a user- ...Conformer selection criteria: All calculated structures were submitted. Our method guarantees that the ensemble represents all structures that satisfy the data and have good vdW packing within a user-defined similarity level (chosen as 1 A).
Conformers calculated total number: 184 / Conformers submitted total number: 184

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