+Open data
-Basic information
Entry | Database: PDB / ID: 1vfp | ||||||
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Title | Crystal structure of the SR CA2+-ATPase with bound AMPPCP | ||||||
Components | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
Keywords | HYDROLASE / Membrane protein / P-type ATPase / HAD fold | ||||||
Function / homology | Function and homology information 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 / P-type Ca2+ transporter / P-type calcium 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 / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Toyoshima, C. / Mizutani, T. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Crystal structure of the calcium pump with a bound ATP analogue. Authors: Toyoshima, C. / Mizutani, T. #1: Journal: Nature / Year: 2000 Title: Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution. Authors: Toyoshima, C. / Nakasako, M. / Nomura, H. / Ogawa, H. #2: Journal: Nature / Year: 2002 Title: Structural changes in the calcium pump accompanying the dissociation of calcium. Authors: Toyoshima, C. / Nomura, H. #3: Journal: FEBS Lett. / Year: 2003 Title: Structural basis of ion pumping by Ca(2+)-ATPase of sarcoplasmic reticulum. Authors: Toyoshima, C. / Nomura, H. / Sugita, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vfp.cif.gz | 357.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vfp.ent.gz | 292.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/1vfp ftp://data.pdbj.org/pub/pdb/validation_reports/vf/1vfp | HTTPS FTP |
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-Related structure data
Related structure data | 1eul S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.65592, 0.74829, 0.09915), Vector: |
-Components
#1: Protein | Mass: 109602.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8 #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.714 Å3/Da / Density % sol: 68.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: microdialysis / pH: 6.1 / Details: PEG400, pH 6.1, MICRODIALYSIS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.72 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 9, 2002 |
Radiation | Monochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 70956 / Num. obs: 70956 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.37 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.45 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.598 / Num. unique all: 5239 / % possible all: 94.2 |
Reflection | *PLUS Lowest resolution: 20 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: P-domain and M3-M10 transmembrane helices of 1EUL 1eul Resolution: 2.9→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 232616.95 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.83 Å2 / ksol: 0.28476 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.252 / Rfactor Rfree: 0.296 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.365 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.34 |