+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25147 | |||||||||
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Title | Structure of shaker-IR | |||||||||
Map data | ||||||||||
Sample |
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Keywords | potassium channel / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / positive regulation of circadian sleep/wake cycle, sleep ...mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / positive regulation of circadian sleep/wake cycle, sleep / regulation of circadian sleep/wake cycle, sleep / detection of visible light / delayed rectifier potassium channel activity / cellular response to dopamine / sleep / axon extension / voltage-gated monoatomic cation channel activity / action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / potassium ion transport / protein homooligomerization / sensory perception of taste / perikaryon / learning or memory / neuron projection / membrane raft / membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Tan X / Bae C | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure of the Shaker Kv channel and mechanism of slow C-type inactivation. Authors: Xiao-Feng Tan / Chanhyung Bae / Robyn Stix / Ana I Fernández-Mariño / Kate Huffer / Tsg-Hui Chang / Jiansen Jiang / José D Faraldo-Gómez / Kenton J Swartz / Abstract: Voltage-activated potassium (Kv) channels open upon membrane depolarization and proceed to spontaneously inactivate. Inactivation controls neuronal firing rates and serves as a form of short-term ...Voltage-activated potassium (Kv) channels open upon membrane depolarization and proceed to spontaneously inactivate. Inactivation controls neuronal firing rates and serves as a form of short-term memory and is implicated in various human neurological disorders. Here, we use high-resolution cryo-electron microscopy and computer simulations to determine one of the molecular mechanisms underlying this physiologically crucial process. Structures of the activated Shaker Kv channel and of its W434F mutant in lipid bilayers demonstrate that C-type inactivation entails the dilation of the ion selectivity filter and the repositioning of neighboring residues known to be functionally critical. Microsecond-scale molecular dynamics trajectories confirm that these changes inhibit rapid ion permeation through the channel. This long-sought breakthrough establishes how eukaryotic K channels self-regulate their functional state through the plasticity of their selectivity filters. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25147.map.gz | 88.6 MB | EMDB map data format | |
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Header (meta data) | emd-25147-v30.xml emd-25147.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_25147.png | 40.9 KB | ||
Filedesc metadata | emd-25147.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25147 | HTTPS FTP |
-Validation report
Summary document | emd_25147_validation.pdf.gz | 478.6 KB | Display | EMDB validaton report |
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Full document | emd_25147_full_validation.pdf.gz | 478.2 KB | Display | |
Data in XML | emd_25147_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_25147_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25147 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25147 | HTTPS FTP |
-Related structure data
Related structure data | 7sipMC 7sj1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25147.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : potassium channel
Entire | Name: potassium channel |
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Components |
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-Supramolecule #1: potassium channel
Supramolecule | Name: potassium channel / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: Potassium voltage-gated channel protein Shaker
Macromolecule | Name: Potassium voltage-gated channel protein Shaker / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 69.47532 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GTMAAVALRE QQLQRNSLDG YGSLPKLSSQ DEEGGAGHGF GGGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPAR RLRYFDPLRN EYFFDRSRPS FDAILYYYQS GGRLRRPVNV PLDVFSEEIK FYELGDQAIN KFREDEGFIK E EERPLPDN ...String: GTMAAVALRE QQLQRNSLDG YGSLPKLSSQ DEEGGAGHGF GGGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPAR RLRYFDPLRN EYFFDRSRPS FDAILYYYQS GGRLRRPVNV PLDVFSEEIK FYELGDQAIN KFREDEGFIK E EERPLPDN EKQRKVWLLF EYPESSQAAR VVAIISVFVI LLSIVIFCLE TLPEFKHYKV FNTTTNGTKI EEDEVPDITD PF FLIETLC IIWFTFELTV RFLACPNKLN FCRDVMNVID IIAIIPYFIT LATVVAEEED TLNLPKAPVS PQDKSSNQAM SLA ILRVIR LVRVFRIFKL SRHSKGLQIL GRTLKASMRE LGLLIFFLFI GVVLFSSAVY FAEAGSENSF FKSIPDAFWW AVVT MTTVG YGDMTPVGVW GKIVGSLCAI AGVLTIALPV PVIVSNFNYF YHRETDQEEM QSQNFNHVTS CPYLPGTLVG QHMKK SSLS ESSSDMMDLD DGVESTPGLT ETHPGRSAVA PFLGAQQQQQ QPVASSLSMS IDKQLQHPLQ QLTQTQLYQQ QQQQQQ QQQ NGFKQQQQQT QQQLQQQQSH TINASAAAAT SGSGSSGLTM RHNNALAVSI ETDV UniProtKB: Potassium voltage-gated channel protein Shaker |
-Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 2 / Number of copies: 32 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Macromolecule #3: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 20 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 16 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229379 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |