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Yorodumi- EMDB-1094: Electron microscopic analysis of KvAP voltage-dependent K+ channe... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1094 | |||||||||
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Title | Electron microscopic analysis of KvAP voltage-dependent K+ channels in an open conformation. | |||||||||
Map data | A map of the KvAP/33H1Fab complex at 10.5 angstrom resolution. A threshold at 1.0 gives 340 kDa. | |||||||||
Sample |
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Biological species | Aeropyrum pernix (archaea) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 10.5 Å | |||||||||
Authors | Jiang QX / Wang DN / MacKinnon R | |||||||||
Citation | Journal: Nature / Year: 2004 Title: Electron microscopic analysis of KvAP voltage-dependent K+ channels in an open conformation. Authors: Qiu-Xing Jiang / Da-Neng Wang / Roderick MacKinnon / Abstract: Voltage-dependent ion channels serve as field-effect transistors by opening a gate in response to membrane voltage changes. The gate's response to voltage is mediated by voltage sensors, which are ...Voltage-dependent ion channels serve as field-effect transistors by opening a gate in response to membrane voltage changes. The gate's response to voltage is mediated by voltage sensors, which are arginine-containing structures that must move with respect to the membrane electric field. We have analysed by electron microscopy a voltage-dependent K(+) channel from Aeropyrum pernix (KvAP). Fab fragments were attached to 'voltage sensor paddles' and identified in the electron microscopy map at 10.5 A resolution. The extracellular surface location of the Fab fragments in the map is consistent with the membrane-depolarized, open conformation of the channel in electrophysiological experiments. Comparison of the map with a crystal structure demonstrates that the voltage sensor paddles are 'up' (that is, near the channel's extracellular surface) and situated at the protein-lipid interface. This finding supports the hypothesis that in response to changes in voltage the sensors move at the protein-lipid interface rather than in a gating pore surrounded by protein. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1094.map.gz | 599.2 KB | EMDB map data format | |
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Header (meta data) | emd-1094-v30.xml emd-1094.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | 1094.gif | 36.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1094 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1094 | HTTPS FTP |
-Validation report
Summary document | emd_1094_validation.pdf.gz | 238.6 KB | Display | EMDB validaton report |
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Full document | emd_1094_full_validation.pdf.gz | 237.6 KB | Display | |
Data in XML | emd_1094_validation.xml.gz | 4.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1094 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1094 | 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_1094.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | A map of the KvAP/33H1Fab complex at 10.5 angstrom resolution. A threshold at 1.0 gives 340 kDa. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : KvAP complexed with 33H1 Fab fragments
Entire | Name: KvAP complexed with 33H1 Fab fragments |
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Components |
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-Supramolecule #1000: KvAP complexed with 33H1 Fab fragments
Supramolecule | Name: KvAP complexed with 33H1 Fab fragments / type: sample / ID: 1000 / Details: none / Oligomeric state: one / Number unique components: 2 |
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Molecular weight | Experimental: 340 KDa / Theoretical: 300 KDa Method: the sequence and the estimate of detergent micelle size |
-Macromolecule #1: KvAP potassium channel
Macromolecule | Name: KvAP potassium channel / type: protein_or_peptide / ID: 1 / Name.synonym: KvAP / Details: one channel / Number of copies: 1 / Oligomeric state: tetramer / Recombinant expression: Yes |
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Source (natural) | Organism: Aeropyrum pernix (archaea) / synonym: A. pernix / Location in cell: plasma membrane |
Molecular weight | Experimental: 120 KDa / Theoretical: 120 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pQE60 |
-Macromolecule #2: 33H1 Fab fragments
Macromolecule | Name: 33H1 Fab fragments / type: protein_or_peptide / ID: 2 / Name.synonym: 33H1Fab / Details: four Fab fragments / Number of copies: 4 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: House Mouse |
Molecular weight | Experimental: 180 KDa / Theoretical: 180 KDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.0 mg/mL |
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Buffer | pH: 7.4 Details: 40 mM KCl, 60 mM NaCl, 20 mM Tris-HCl pH 7.4, 5.0 mM DM |
Staining | Type: NEGATIVE / Details: mix with equal volume of 65% ammonium molybdate |
Grid | Details: 400 mesh grids with holey carbon film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home-made / Method: 8 |
-Electron microscopy
Microscope | FEI/PHILIPS CM200T |
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Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: corrected at 200000 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 37 / Average electron dose: 20 e/Å2 / Od range: 1.2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.1 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Oxford / Specimen holder model: OTHER |
-Image processing
Details | the holes in the carbon film were covered with a thin-layer of carbon film. |
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CTF correction | Details: each particle |
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC SPIDER / Number images used: 21379 |
Final two d classification | Number classes: 496 |