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Yorodumi- EMDB-9026: The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid n... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9026 | |||||||||
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Title | The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid nanodiscs, transmembrane domain of subunit alpha | |||||||||
Map data | Kv1.2-2.1 paddle chimera in lipid nanodiscs, transmembrane domain | |||||||||
Sample |
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Keywords | MEMBRANE PROTEIN / transport protein / potassium channel / lipid nanodisc | |||||||||
Function / homology | Function and homology information optic nerve structural organization / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / paranodal junction / potassium ion export across plasma membrane / regulation of circadian sleep/wake cycle, non-REM sleep / axon initial segment / delayed rectifier potassium channel activity / corpus callosum development ...optic nerve structural organization / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / paranodal junction / potassium ion export across plasma membrane / regulation of circadian sleep/wake cycle, non-REM sleep / axon initial segment / delayed rectifier potassium channel activity / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / outward rectifier potassium channel activity / juxtaparanode region of axon / optic nerve development / neuronal cell body membrane / regulation of dopamine secretion / voltage-gated potassium channel activity / lamellipodium membrane / kinesin binding / neuronal action potential / calyx of Held / voltage-gated potassium channel complex / axon terminus / sensory perception of pain / potassium ion transmembrane transport / protein localization to plasma membrane / protein homooligomerization / potassium ion transport / cerebral cortex development / lamellipodium / presynaptic membrane / perikaryon / postsynaptic membrane / transmembrane transporter binding / endosome / protein heterodimerization activity / axon / dendrite / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Matthies D / Bae C | |||||||||
Citation | Journal: Elife / Year: 2018 Title: Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs. Authors: Doreen Matthies / Chanhyung Bae / Gilman Es Toombes / Tara Fox / Alberto Bartesaghi / Sriram Subramaniam / Kenton Jon Swartz / Abstract: Voltage-activated potassium (Kv) channels open to conduct K ions in response to membrane depolarization, and subsequently enter non-conducting states through distinct mechanisms of inactivation. X- ...Voltage-activated potassium (Kv) channels open to conduct K ions in response to membrane depolarization, and subsequently enter non-conducting states through distinct mechanisms of inactivation. X-ray structures of detergent-solubilized Kv channels appear to have captured an open state even though a non-conducting C-type inactivated state would predominate in membranes in the absence of a transmembrane voltage. However, structures for a voltage-activated ion channel in a lipid bilayer environment have not yet been reported. Here we report the structure of the Kv1.2-2.1 paddle chimera channel reconstituted into lipid nanodiscs using single-particle cryo-electron microscopy. At a resolution of ~3 Å for the cytosolic domain and ~4 Å for the transmembrane domain, the structure determined in nanodiscs is similar to the previously determined X-ray structure. Our findings show that large differences in structure between detergent and lipid bilayer environments are unlikely, and enable us to propose possible structural mechanisms for C-type inactivation. | |||||||||
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_9026.map.gz | 131.9 MB | EMDB map data format | |
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Header (meta data) | emd-9026-v30.xml emd-9026.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_9026.png | 89.1 KB | ||
Masks | emd_9026_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-9026.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9026 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9026 | HTTPS FTP |
-Related structure data
Related structure data | 6ebmMC 9024C 9025C 6ebkC 6eblC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9026.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Kv1.2-2.1 paddle chimera in lipid nanodiscs, transmembrane domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_9026_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Voltage-activated potassium channel Kv1.2-2.1 paddle chimera in l...
Entire | Name: Voltage-activated potassium channel Kv1.2-2.1 paddle chimera in lipid nanodiscs, transmembrane domain |
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Components |
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-Supramolecule #1: Voltage-activated potassium channel Kv1.2-2.1 paddle chimera in l...
Supramolecule | Name: Voltage-activated potassium channel Kv1.2-2.1 paddle chimera in lipid nanodiscs, transmembrane domain type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 385 KDa |
-Macromolecule #1: Potassium voltage-gated channel subfamily A member 2,Potassium vo...
Macromolecule | Name: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily B member 2 chimera type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 58.905828 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MAHHHHHHHH ENLYFQGSMT VATGDPVDEA AAHPGHPQDT YDPEADHECC ERVVINISGL RFETQLKTLA QFPETLLGDP KKRMRYFDP LRNEYFFDRN RPSFDAILYY YQSGGRLRRP VNVPLDIFSE EIRFYELGEE AMEMFREDEG YIKEEERPLP E NEFQRQVW ...String: MAHHHHHHHH ENLYFQGSMT VATGDPVDEA AAHPGHPQDT YDPEADHECC ERVVINISGL RFETQLKTLA QFPETLLGDP KKRMRYFDP LRNEYFFDRN RPSFDAILYY YQSGGRLRRP VNVPLDIFSE EIRFYELGEE AMEMFREDEG YIKEEERPLP E NEFQRQVW LLFEYPESSG PARIIAIVSV MVILISIVSF CLETLPIFRD ENEDMHGGGV TFHTYSQSTI GYQQSTSFTD PF FIVETLC IIWFSFEFLV RFFACPSKAG FFTNIMNIID IVAIIPYYVT IFLTESNKSV LQFQNVRRVV QIFRIMRILR IFK LSRHSK GLQILGQTLK ASMRELGLLI FFLFIGVILF SSAVYFAEAD ERDSQFPSIP DAFWWAVVSM TTVGYGDMVP TTIG GKIVG SLCAIAGVLT IALPVPVIVS NFNYFYHRET EGEEQAQYLQ VTSCPKIPSS PDLKKSRSAS TISKSDYMEI QEGVN NSNE DFREENLKTA NCTLANTNYV NITKMLTDV UniProtKB: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 2, Potassium voltage-gated channel subfamily A member 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP Details: A 3 microliter sample was applied to a plasma-cleaned grid and blotted for 10 seconds.. | ||||||||||||
Details | Kv1.2-2.1 paddle chimera in lipid nanodiscs, transmembrane alpha subunits |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 3085 / Average exposure time: 15.2 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 281021 |
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Startup model | Type of model: OTHER Details: An initial model was created from negatively stained single particle electron microscopy. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final 3D classification | Number classes: 2 / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 65745 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 123 |
Output model | PDB-6ebm: |