+Open data
-Basic information
Entry | Database: PDB / ID: 2agv | ||||||
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Title | Crystal structure of the SR CA2+-ATPASE with BHQ and TG | ||||||
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: 2.4 Å | ||||||
Authors | Toyoshima, C. / Obara, K. / Norimatsu, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Inaugural Article: Structural role of countertransport revealed in Ca2+ pump crystal structure in the absence of Ca2+. Authors: Obara, K. / Miyashita, N. / Xu, C. / Toyoshima, I. / Sugita, Y. / Inesi, G. / Toyoshima, C. #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. #4: Journal: Nature / Year: 2004 Title: Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues Authors: Toyoshima, C. / Nomura, H. / Tsuda, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2agv.cif.gz | 403 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2agv.ent.gz | 323.3 KB | Display | PDB format |
PDBx/mmJSON format | 2agv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2agv ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2agv | HTTPS FTP |
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-Related structure data
Related structure data | 1iwoS 1wpe 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:
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 260 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PTY / #6: 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: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.468 Å3/Da / Density % sol: 65.9 % |
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Crystal grow | Temperature: 283 K / Method: microdialysis / pH: 6.1 / Details: PEG400, pH 6.10, MICRODIALYSIS, temperature 283K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.75 Å | ||||||||||||
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 | Wavelength: 0.75 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 2.4→20 Å / Num. all: 114354 / Num. obs: 114125 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 29.3 | ||||||||||||
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 4.5 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3 CYTOPLASMIC DOMAINS OF CA2+-ATPASE IN 1IWO Resolution: 2.4→14.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3405795.84 / 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: 39.3843 Å2 / ksol: 0.31951 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→14.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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