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- PDB-2zbg: Calcium pump crystal structure with bound AlF4 and TG in the abse... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zbg | ||||||
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Title | Calcium pump crystal structure with bound AlF4 and TG in the absence of calcium | ||||||
![]() | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
![]() | HYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / ATP-BINDING / CALCIUM TRANSPORT / ENDOPLASMIC RETICULUM / ION TRANSPORT / MAGNESIUM / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SARCOPLASMIC RETICULUM / TRANSMEMBRANE / TRANSPORT | ||||||
Function / homology | ![]() 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 / intracellular calcium ion homeostasis / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Toyoshima, C. / Ogawa, H. / Norimatsu, Y. | ||||||
![]() | ![]() Title: How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump Authors: Toyoshima, C. / Norimatsu, Y. / Iwasawa, S. / Tsuda, T. / Ogawa, H. #1: ![]() 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: ![]() Title: Structural changes in the calcium pump accompanying the dissociation of calcium Authors: Toyoshima, C. / Nomura, H. #3: ![]() Title: Crystal structure of the calcium pump with a bound ATP analogue Authors: Toyoshima, C. / Mizutani, T. #4: ![]() Title: Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues Authors: Toyoshima, C. / Nomura, H. / Tsuda, T. #5: ![]() Title: Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+) Authors: Obara, K. / Miyashita, N. / Xu, C. / Toyoshima, I. / Sugita, Y. / Inesi, G. / Toyoshima, C. #6: ![]() Title: Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors Authors: Takahashi, M. / Kondou, Y. / Toyoshima, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.5 KB | Display | ![]() |
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PDB format | ![]() | 165.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.3 KB | Display | ![]() |
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Full document | ![]() | 516.6 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 37.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zbeC ![]() 2zbfC ![]() 1wpgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 109628.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ALF / |
#4: Chemical | ChemComp-TG1 / |
#5: Water | ChemComp-HOH / |
Sequence details | THE C-TERMINAL RESIDUES IN UNP ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, ...THE C-TERMINAL RESIDUES IN UNP ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, THERE IS ONLY ONE C-TERMINAL RESIDUE 994 GLY. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.48 % |
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Crystal grow | Temperature: 283 K / Method: microdialysis / pH: 6.1 / Details: pH 6.1, MICRODIALYSIS, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2006 |
Radiation | Monochromator: ROTATED-INCLINED DOUBLE- CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. all: 55341 / Num. obs: 55231 / % possible obs: 99.8 % / Observed criterion σ(I): -2 / Redundancy: 7.2 % / Biso Wilson estimate: 66.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 2.55→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2 / Num. unique all: 3158 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WPG Resolution: 2.55→11.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1941905.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 86.8545 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→11.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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