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- PDB-3tlm: Crystal Structure of Endoplasmic Reticulum Ca2+-ATPase (SERCA) Fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tlm | ||||||
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Title | Crystal Structure of Endoplasmic Reticulum Ca2+-ATPase (SERCA) From Bovine Muscle | ||||||
![]() | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | ||||||
![]() | HYDROLASE / SERCA / Ca-ATPase / Calcium transporter / Ca / Fast-twitch muscle | ||||||
Function / homology | ![]() maintenance of mitochondrion location / relaxation of skeletal muscle / positive regulation of endoplasmic reticulum calcium ion concentration / positive regulation of mitochondrial calcium ion concentration / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of endoplasmic reticulum calcium ion concentration / P-type proton-exporting transporter activity ...maintenance of mitochondrion location / relaxation of skeletal muscle / positive regulation of endoplasmic reticulum calcium ion concentration / positive regulation of mitochondrial calcium ion concentration / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of endoplasmic reticulum calcium ion concentration / P-type proton-exporting transporter activity / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type Ca2+ transporter / P-type calcium transporter activity / apoptotic mitochondrial changes / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / sarcoplasmic reticulum membrane / calcium ion transmembrane transport / intracellular calcium ion homeostasis / membrane => GO:0016020 / calcium ion binding / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sacchetto, R. / Bertipaglia, I. / Giannetti, S. / Cendron, L. / Mascarello, F. / Damiani, E. / Carafoli, E. / Zanotti, G. | ||||||
![]() | ![]() Title: Crystal structure of sarcoplasmic reticulum Ca(2+)-ATPase (SERCA) from bovine muscle. Authors: Sacchetto, R. / Bertipaglia, I. / Giannetti, S. / Cendron, L. / Mascarello, F. / Damiani, E. / Carafoli, E. / Zanotti, G. #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: The structural basis of calcium transport by the calcium pump. Authors: Olesen, C. / Picard, M. / Winther, A.M. / Gyrup, C. / Morth, J.P. / Oxvig, C. / Moller, J.V. / Nissen, P. #3: Journal: Physiol Rev / Year: 2009 Title: Calcium pumps in health and disease. Authors: Brini, M. / Carafoli, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209 KB | Display | ![]() |
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PDB format | ![]() | 162.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773 KB | Display | ![]() |
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Full document | ![]() | 831.1 KB | Display | |
Data in XML | ![]() | 42.5 KB | Display | |
Data in CIF | ![]() | 57.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1t5sS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 109346.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cutaneus trunci muscle / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 38 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-K / | #5: Chemical | ChemComp-ACP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.32 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 220mM sodium acetate, 4% t-butanol, 5mM mercaptoethanol, 15% glycerol, 6-7% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→76.61 Å / Num. all: 35944 / Num. obs: 35546 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 60.2 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.5 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1T5S Resolution: 2.95→41.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2964064.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0516 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→41.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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