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Yorodumi- EMDB-1605: Solution structure of the KdpFABC P-type ATPase from Escherichia ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1605 | |||||||||
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Title | Solution structure of the KdpFABC P-type ATPase from Escherichia coli by electron microscopic single particle analysis | |||||||||
Map data | Volume of the KdpFABC P-type ATPase | |||||||||
Sample |
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Keywords | KdpFABC / P-type ATPase / potassium transport / single particle analysis / electron microscopy. | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Heitkamp T / Bottcher B / Greie J-C | |||||||||
Citation | Journal: J Struct Biol / Year: 2009 Title: Solution structure of the KdpFABC P-type ATPase from Escherichia coli by electron microscopic single particle analysis. Authors: Thomas Heitkamp / Bettina Böttcher / Jörg-Christian Greie / Abstract: The K+-translocating KdpFABC complex from Escherichia coli functions as a high affinity potassium uptake system and belongs to the superfamily of P-type ATPases, although it exhibits some unique ...The K+-translocating KdpFABC complex from Escherichia coli functions as a high affinity potassium uptake system and belongs to the superfamily of P-type ATPases, although it exhibits some unique features. It comprises four subunits, and the sites of ATP hydrolysis and substrate transport are located on two different polypeptides. No structural data are so far available for elucidating the correspondingly unique mechanism of coupling ion transport and catalysis in this P-type ATPase. By use of electron microscopy and single particle analysis of negatively stained, solubilized KdpFABC complexes, we solved the structure of the complex at a resolution of 19A, which allowed us to model the arrangement of subunits within the holoenzyme and, thus, to identify the interfaces between subunits. The model showed that the K+-translocating KdpA subunit is in close contact with the transmembrane region of the ATP-hydrolyzing subunit KdpB. The cytosolic C-terminal domain of the KdpC subunit, which is assumed to play a role in cooperative ATP binding together with KdpB, is located in close vicinity to the nucleotide binding domain of KdpB. Overall, the arrangement of subunits agrees with biochemical data and the predictions on subunit interactions. | |||||||||
History |
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-Structure visualization
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1605.map.gz | 167 KB | EMDB map data format | |
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Header (meta data) | emd-1605-v30.xml emd-1605.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_1605.gif | 91.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1605 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1605 | HTTPS FTP |
-Validation report
Summary document | emd_1605_validation.pdf.gz | 195.3 KB | Display | EMDB validaton report |
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Full document | emd_1605_full_validation.pdf.gz | 194.5 KB | Display | |
Data in XML | emd_1605_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1605 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1605 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1605.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Volume of the KdpFABC P-type ATPase | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : KdpFABC P-type ATPase
Entire | Name: KdpFABC P-type ATPase |
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Components |
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-Supramolecule #1000: KdpFABC P-type ATPase
Supramolecule | Name: KdpFABC P-type ATPase / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 154 KDa |
-Macromolecule #1: KdpA-subunit
Macromolecule | Name: KdpA-subunit / type: protein_or_peptide / ID: 1 / Name.synonym: KdpA-subunit / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: membrane |
Molecular weight | Theoretical: 59 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pGS4 |
-Macromolecule #2: KdpB-subunit
Macromolecule | Name: KdpB-subunit / type: protein_or_peptide / ID: 2 / Name.synonym: KdpB-subunit / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: membrane |
Molecular weight | Theoretical: 72 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pGS4 |
-Macromolecule #3: KdpC-subunit
Macromolecule | Name: KdpC-subunit / type: protein_or_peptide / ID: 3 / Name.synonym: KdpC-subunit / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: membrane |
Molecular weight | Theoretical: 21 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pGS4 |
-Macromolecule #4: KdpF-subunit
Macromolecule | Name: KdpF-subunit / type: protein_or_peptide / ID: 4 / Name.synonym: KdpF-subunit / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: membrane |
Molecular weight | Theoretical: 3 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pGS4 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.005 mg/mL |
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Buffer | pH: 6 Details: 50 mM MES pH 6.0, 50 mM NaCl, 5 mM MgCl2, 5 mM CaCl2 |
Staining | Type: NEGATIVE Details: applied to freshly glow-discharged carbon-coated copper grids (400 mesh). Staining with 2 % (w/v) uranylacetic acid |
Grid | Details: 400 mesh copper grid, carbon coated |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM120T |
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Temperature | Min: 95 K / Max: 295 K / Average: 295 K |
Alignment procedure | Legacy - Astigmatism: manually at 200000 on carbon film |
Date | Jul 20, 2004 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 90 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 100 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 48000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.864 µm / Nominal defocus min: 0.432 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder: room temperature holder / Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Details | started with angular reconstitution in IMAGIC (25 class averages) followed by projection matching in Spider (global search in 10 degree steps followed by local search in 2 degree steps) |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC Spider / Number images used: 10040 |