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Yorodumi- PDB-8xmi: Potassium transporter KtrAB from Bacillus subtilis in ATP-bound s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xmi | ||||||
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Title | Potassium transporter KtrAB from Bacillus subtilis in ATP-bound state with addition of EDTA and EGTA, C1 symmetry | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / KtrAB / RCK / potassium / transporter | ||||||
Function / homology | Function and homology information potassium:chloride symporter activity / monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Chang, Y.K. / Chiang, W.T. / Hu, N.J. / Tsai, M.D. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB Authors: Chiang, W.T. / Chang, Y.K. / Hui, W.H. / Chang, S.W. / Liao, C.Y. / Chang, Y.C. / Chen, C.J. / Wang, W.C. / Lai, C.C. / Wang, C.H. / Luo, S.Y. / Huang, Y.P. / Chou, S.H. / Horng, T.L. / Hou, ...Authors: Chiang, W.T. / Chang, Y.K. / Hui, W.H. / Chang, S.W. / Liao, C.Y. / Chang, Y.C. / Chen, C.J. / Wang, W.C. / Lai, C.C. / Wang, C.H. / Luo, S.Y. / Huang, Y.P. / Chou, S.H. / Horng, T.L. / Hou, M.H. / Muench, S.P. / Chen, R.S. / Tsai, M.D. / Hu, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xmi.cif.gz | 568.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xmi.ent.gz | 477.5 KB | Display | PDB format |
PDBx/mmJSON format | 8xmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/8xmi ftp://data.pdbj.org/pub/pdb/validation_reports/xm/8xmi | HTTPS FTP |
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-Related structure data
Related structure data | 38478MC 8k16C 8k1kC 8k1sC 8k1tC 8k1uC 8xmhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 24916.760 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080 #2: Protein | Mass: 48471.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ktrB, yubG, BSU31100 / Production host: Escherichia coli (E. coli) / References: UniProt: O32081 #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-K / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 Details: 20 mM Tris-HCl pH 8.0, 70 mM NaCl, 30 mM KCl, 0.75 mM 6-cyclohexyl-1-hexyl-beta-D-maltoside, 2 mM EDTA, 1 mM EGTA, 1 mM ATP | ||||||||||||||||||||||||||||
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1400 nm |
Image recording | Average exposure time: 2 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8613 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 527427 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 4J7C Accession code: 4J7C / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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