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Yorodumi- PDB-2kyv: Hybrid solution and solid-state NMR structure ensemble of phospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kyv | ||||||
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Title | Hybrid solution and solid-state NMR structure ensemble of phospholamban pentamer | ||||||
Components | Phospholamban | ||||||
Keywords | MEMBRANE PROTEIN / phospholamban / solid state NMR / hybrid method | ||||||
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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / SOLID-STATE NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Verardi, R. / Shi, L. / Traaseth, N.J. / Veglia, G. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kyv.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kyv.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 2kyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/2kyv ftp://data.pdbj.org/pub/pdb/validation_reports/ky/2kyv | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
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NMR experiment |
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-Sample preparation
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-Data collection
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR constraints | NOE 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer 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 rms | Distance rms dev: 0.05 Å / Distance rms dev error: 0.003 Å |