+Open data
-Basic information
Entry | Database: PDB / ID: 4y3u | ||||||
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Title | The structure of phospholamban bound to the calcium pump SERCA1a | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Ca-ATPase / SERCA1a | ||||||
Function / homology | Function and homology information Ion homeostasis / Ion transport by P-type ATPases / 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 / acrosome assembly / negative regulation of calcium ion transmembrane transporter activity ...Ion homeostasis / Ion transport by P-type ATPases / 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 / acrosome assembly / negative regulation of calcium ion transmembrane transporter activity / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of calcium ion import / P-type Ca2+ transporter / P-type calcium transporter activity / ATPase inhibitor activity / negative regulation of ATP-dependent activity / regulation of cardiac muscle cell contraction / cardiac muscle tissue development / I band / negative regulation of heart rate / muscle cell cellular homeostasis / regulation of calcium ion transport / endoplasmic reticulum-Golgi intermediate compartment / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Notch signaling pathway / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / mitochondrial membrane / intracellular calcium ion homeostasis / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Canis familiaris (dog) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.51 Å | ||||||
Authors | Hurley, T.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2013 Title: The structural basis for phospholamban inhibition of the calcium pump in sarcoplasmic reticulum. Authors: Akin, B.L. / Hurley, T.D. / Chen, Z. / Jones, L.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y3u.cif.gz | 403.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y3u.ent.gz | 335.4 KB | Display | PDB format |
PDBx/mmJSON format | 4y3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/4y3u ftp://data.pdbj.org/pub/pdb/validation_reports/y3/4y3u | HTTPS FTP |
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-Related structure data
Related structure data | 4kytSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: MuscleSkeletal muscle / Tissue: skeletal muscle / References: UniProt: P04191, EC: 3.6.3.8 |
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#2: Protein/peptide | Mass: 5859.158 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis familiaris (dog) / Gene: PLN / Plasmid: PVL1393 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61012 |
#3: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This is a second copy of phospholamban bound in this structure, but the side chain electron density is insufficient to assign the correct sequence register Source: (gene. exp.) Canis familiaris (dog) / Gene: PLN / Production host: Spodoptera frugiperda (fall armyworm) |
#4: Chemical | ChemComp-K / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 UL OF SERCA1A AT 15 MG/ML IN 2% N- NONYL-BETA-D-MALTOPYRANOSIDE (NONYL MALTOSIDE) (ANATRACE), 20% GLYCEROL, 100 MM MOPS (PH 7.0), 0.12 M SUCROSE, 80 MM KCL, 3 MM MGCL2, AND 2.8 MM EGTA WAS ...Details: 1 UL OF SERCA1A AT 15 MG/ML IN 2% N- NONYL-BETA-D-MALTOPYRANOSIDE (NONYL MALTOSIDE) (ANATRACE), 20% GLYCEROL, 100 MM MOPS (PH 7.0), 0.12 M SUCROSE, 80 MM KCL, 3 MM MGCL2, AND 2.8 MM EGTA WAS MIXED WITH 1 UL OF PHOSPHOLAMBAN AT 2.1 MG/ML IN 20 MM MOPS (PH 7.2), 20% GLYCEROL, AND 0.1 % DECYLMALTOSIDE OR 0.01% DODECYL MALTOSIDE. THIS PROTEIN MIXTURE WAS THEN ADDED TO AN EQUAL VOLUME OF CRYSTALLIZATION LIQUOR; 15 % GLYCEROL, 17% (W/V) PEG-2000, 200MM NAOAC, AND 5 MM BETA-MERCOPTOETHANOL) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 23282 / % possible obs: 99 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.46 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.47 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 4KYT Resolution: 3.51→48.79 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.852 / SU B: 56.647 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.592 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 135.931 Å2
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Refinement step | Cycle: 1 / Resolution: 3.51→48.79 Å
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