+Open data
-Basic information
Entry | Database: PDB / ID: 1wpg | ||||||
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Title | Crystal structure of the SR CA2+-ATPase with MGF4 | ||||||
Components | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / regulation of striated muscle contraction / negative 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 / regulation of striated muscle contraction / negative 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: 2.3 Å | ||||||
Authors | Toyoshima, C. / Nomura, H. / Tsuda, T. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues Authors: Toyoshima, C. / Nomura, H. / Tsuda, 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: Nature / Year: 2004 Title: Crystal structure of the calcium pump with a bound ATP analogue Authors: Toyoshima, C. / Mizutani, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wpg.cif.gz | 784.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wpg.ent.gz | 639.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/1wpg ftp://data.pdbj.org/pub/pdb/validation_reports/wp/1wpg | HTTPS FTP |
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-Related structure data
Related structure data | 2zbdC 1fquS 1wpe 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 109602.578 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle (white) / References: UniProt: P04191, EC: 3.6.3.8 |
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-Non-polymers , 6 types, 714 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-MF4 / #5: Chemical | ChemComp-ADP / #6: Chemical | ChemComp-TG1 / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE C-TERMINAL RESIDUES IN SWS ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, ...THE C-TERMINAL RESIDUES IN SWS ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, THERE IS ONLY ONE C-TERMINAL RESIDUE 994 G. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 63.17 % |
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Crystal grow | Method: microdialysis / pH: 6.1 / Details: PEG400, pH 6.10, MICRODIALYSIS |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: ROTATED-INCLINED DOUBLE- CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→20 Å / Num. obs: 250560 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 5.07 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 25.14 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.432 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3 CYTOPLASMIC DOMAINS OF CA2+-ATPASE IN 1FQU Resolution: 2.3→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 410979.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.47 Å2 / ksol: 0.328798 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→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: 2.3→2.44 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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