+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28487 | |||||||||
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Title | Eag Kv channel with voltage sensor in the up conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | voltage-gated potassium channel / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / parallel fiber to Purkinje cell synapse / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / nuclear inner membrane ...Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / parallel fiber to Purkinje cell synapse / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / nuclear inner membrane / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / regulation of synaptic vesicle exocytosis / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / phosphatidylinositol bisphosphate binding / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / startle response / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / Smooth Muscle Contraction / axolemma / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / eNOS activation / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / 14-3-3 protein binding / calcium channel complex / potassium ion transmembrane transport / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / cellular response to calcium ion / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / regulation of membrane potential / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / postsynaptic density membrane / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / potassium ion transport / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Mandala VS / MacKinnon R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Voltage-sensor movements in the Eag Kv channel under an applied electric field. Authors: Venkata Shiva Mandala / Roderick MacKinnon / Abstract: Voltage-dependent ion channels regulate the opening of their pores by sensing the membrane voltage. This process underlies the propagation of action potentials and other forms of electrical activity ...Voltage-dependent ion channels regulate the opening of their pores by sensing the membrane voltage. This process underlies the propagation of action potentials and other forms of electrical activity in cells. The voltage dependence of these channels is governed by the transmembrane displacement of the positive charged S4 helix within their voltage-sensor domains. We use cryo-electron microscopy to visualize this movement in the mammalian Eag voltage-dependent potassium channel in lipid membrane vesicles with a voltage difference across the membrane. Multiple structural configurations show that the applied electric field displaces S4 toward the cytoplasm by two helical turns, resulting in an extended interfacial helix near the inner membrane leaflet. The position of S4 in this down conformation is sterically incompatible with an open pore, thus explaining how movement of the voltage sensor at hyperpolarizing membrane voltages locks the pore shut in this kind of voltage-dependent K (K) channel. The structures solved in lipid bilayer vesicles detail the intricate interplay between K channels and membranes, from showing how arginines are stabilized deep within the membrane and near phospholipid headgroups, to demonstrating how the channel reshapes the inner leaflet of the membrane itself. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28487.map.gz | 59.2 MB | EMDB map data format | |
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Header (meta data) | emd-28487-v30.xml emd-28487.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28487_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_28487.png | 103.5 KB | ||
Filedesc metadata | emd-28487.cif.gz | 5.9 KB | ||
Others | emd_28487_additional_1.map.gz emd_28487_half_map_1.map.gz emd_28487_half_map_2.map.gz | 30.8 MB 59 MB 59 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28487 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28487 | HTTPS FTP |
-Validation report
Summary document | emd_28487_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_28487_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_28487_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_28487_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28487 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28487 | HTTPS FTP |
-Related structure data
Related structure data | 8eowMC 8ep0C 8ep1C C: citing same article (ref.) M: atomic model generated by this map |
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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_28487.map.gz / Format: CCP4 / Size: 64 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: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_28487_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28487_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28487_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+
Entire | Name: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+ |
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Components |
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-Supramolecule #1: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+
Supramolecule | Name: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+ type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Macromolecule #1: Potassium voltage-gated channel subfamily H member 1
Macromolecule | Name: Potassium voltage-gated channel subfamily H member 1 / 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: 81.664094 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LVAPQNTFLE NIVRRSNDTN FVLGNAQIVD WPIVYSNDGF CKLSGYHRAE VMQKSSACSF MYGELTDKDT VEKVRQTFEN YEMNSFEIL MYKKNRTPVW FFVKIAPIRN EQDKVVLFLC TFSDITAFKQ PIEDDSCKGW GKFARLTRAL TSSRGVLQQL A PSVQKGEN ...String: LVAPQNTFLE NIVRRSNDTN FVLGNAQIVD WPIVYSNDGF CKLSGYHRAE VMQKSSACSF MYGELTDKDT VEKVRQTFEN YEMNSFEIL MYKKNRTPVW FFVKIAPIRN EQDKVVLFLC TFSDITAFKQ PIEDDSCKGW GKFARLTRAL TSSRGVLQQL A PSVQKGEN VHKHSRLAEV LQLGSDILPQ YKQEAPKTPP HIILHYCVFK TTWDWIILIL TFYTAILVPY NVSFKTRQNN VA WLVVDSI VDVIFLVDIV LNFHTTFVGP AGEVISDPKL IRMNYLKTWF VIDLLSCLPY DVINAFENVD EGISSLFSSL KVV RLLRLG RVARKLDHYI EYGAAVLVLL VCVFGLAAHW MACIWYSIGD YEIFDEDTKT IRNNSWLYQL ALDIGTPYQF NGSG SGKWE GGPSKNSVYI SSLYFTMTSL TSVGFGNIAP STDIEKIFAV AIMMIGSLLY ATIFGNVTTI FQQMYANTNR YHEML NSVR DFLKLYQVPK GLSERVMDYI VSTWSMSRGI DTEKVLQICP KDMRADICVH LNRKVFKEHP AFRLASDGCL RALAME FQT VHCAPGDLIY HAGESVDSLC FVVSGSLEVI QDDEVVAILG KGDVFGDVFW KEATLAQSCA NVRALTYCDL HVIKRDA LQ KVLEFYTAFS HSFSRNLILT YNLRKRIVFR KISDVKREEE ERMKRKNEAP LILPPDHPVR RLFQRFRQQK E UniProtKB: Voltage-gated delayed rectifier potassium channel KCNH1 |
-Macromolecule #2: Calmodulin-1
Macromolecule | Name: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.063608 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EEQIAEFKEA FSLFDKDGDG TITTKELGTV MRSLGQNPTE AELQDMINEV DADGNGTIDF PEFLTMMARK MKDTDSEEEI REAFRVFDK DGNGYISAAE LRHVMTNLGE KLTDEEVDEM IREADIDGDG QVNYEEFVQM MTA UniProtKB: Calmodulin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 22 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 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: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |