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- EMDB-9024: The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid n... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9024 | |||||||||
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Title | The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid nanodiscs | |||||||||
![]() | Kv1.2-2.1 paddle chimera in lipid nanodiscs, entire protein | |||||||||
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Function / homology | ![]() optic nerve structural organization / pinceau fiber / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Matthies D / Bae C | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 132.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
Images | ![]() | 154.4 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() | 200.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ebkMC ![]() 9025C ![]() 9026C ![]() 6eblC ![]() 6ebmC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Kv1.2-2.1 paddle chimera in lipid nanodiscs, entire protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Projections & Slices |
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Density Histograms |
-Additional map: Kv1.2-2.1 paddle chimera in lipid nanodiscs, additional map
File | emd_9024_additional.map | ||||||||||||
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Annotation | Kv1.2-2.1 paddle chimera in lipid nanodiscs, additional map | ||||||||||||
Projections & Slices |
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Density Histograms |
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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 |
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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 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 385 KDa |
-Macromolecule #1: Voltage-gated potassium channel subunit beta-2
Macromolecule | Name: Voltage-gated potassium channel subunit beta-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 37.339059 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MVQFYRNLGK SGLRVSCLGL GTWVTFGGQI TDEMAEHLMT LAYDNGINLF DTAEVYAAGK AEVVLGNIIK KKGWRRSSLV ITTKIFWGG KAETERGLSR KHIIEGLKAS LERLQLEYVD VVFANRPDPN TPMEETVRAM THVINQGMAM YWGTSRWSSM E IMEAYSVA ...String: MVQFYRNLGK SGLRVSCLGL GTWVTFGGQI TDEMAEHLMT LAYDNGINLF DTAEVYAAGK AEVVLGNIIK KKGWRRSSLV ITTKIFWGG KAETERGLSR KHIIEGLKAS LERLQLEYVD VVFANRPDPN TPMEETVRAM THVINQGMAM YWGTSRWSSM E IMEAYSVA RQFNLIPPIC EQAEYHMFQR EKVEVQLPEL FHKIGVGAMT WSPLACGIVS GKYDSGIPPY SRASLKGYQW LK DKILSEE GRRQQAKLKE LQAIAERLGC TLPQLAIAWC LRNEGVSSVL LGASNAEQLM ENIGAIQVLP KLSSSIVHEI DSI LGNKPY SKKDYRS UniProtKB: ![]() |
-Macromolecule #2: 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: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 58.905828 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 |
-Macromolecule #3: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Macromolecule | Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAP |
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Molecular weight | Theoretical: 743.405 Da |
Chemical component information | ![]() ChemComp-NAP: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 128 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
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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![]() |