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Yorodumi- EMDB-8215: Single particle cryo-EM structure of the voltage-gated K+ channel... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8215 | ||||||||||||
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Title | Single particle cryo-EM structure of the voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin | ||||||||||||
Map data | Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin | ||||||||||||
Sample |
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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 / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / delayed rectifier potassium channel activity / CaM pathway / Cam-PDE 1 activation ...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 / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / delayed rectifier potassium channel activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / parallel fiber to Purkinje cell synapse / nuclear inner membrane / Calmodulin induced events / regulation of synaptic vesicle endocytosis / 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 / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / phosphatidylinositol bisphosphate binding / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / response to corticosterone / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / startle response / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / axolemma / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / potassium ion transmembrane transport / monoatomic ion transmembrane transport / 14-3-3 protein binding / calcium channel complex / response to amphetamine / substantia nigra development / cellular response to calcium ion / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / regulation of membrane potential / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.78 Å | ||||||||||||
Authors | Whicher JR / MacKinnon R | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Science / Year: 2016 Title: Structure of the voltage-gated K⁺ channel Eag1 reveals an alternative voltage sensing mechanism. Authors: Jonathan R Whicher / Roderick MacKinnon / Abstract: Voltage-gated potassium (K(v)) channels are gated by the movement of the transmembrane voltage sensor, which is coupled, through the helical S4-S5 linker, to the potassium pore. We determined the ...Voltage-gated potassium (K(v)) channels are gated by the movement of the transmembrane voltage sensor, which is coupled, through the helical S4-S5 linker, to the potassium pore. We determined the single-particle cryo-electron microscopy structure of mammalian K(v)10.1, or Eag1, bound to the channel inhibitor calmodulin, at 3.78 angstrom resolution. Unlike previous K(v) structures, the S4-S5 linker of Eag1 is a five-residue loop and the transmembrane segments are not domain swapped, which suggest an alternative mechanism of voltage-dependent gating. Additionally, the structure and position of the S4-S5 linker allow calmodulin to bind to the intracellular domains and to close the potassium pore, independent of voltage-sensor position. The structure reveals an alternative gating mechanism for K(v) channels and provides a template to further understand the gating properties of Eag1 and related channels. | ||||||||||||
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_8215.map.gz | 6.6 MB | EMDB map data format | |
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Header (meta data) | emd-8215-v30.xml emd-8215.xml | 25.1 KB 25.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8215_fsc.xml | 10.8 KB | Display | FSC data file |
Images | emd_8215.png | 146.2 KB | ||
Others | emd_8215_additional_1.map.gz emd_8215_additional_2.map.gz emd_8215_additional_3.map.gz | 59 MB 6.6 MB 59 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8215 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8215 | HTTPS FTP |
-Validation report
Summary document | emd_8215_validation.pdf.gz | 372.4 KB | Display | EMDB validaton report |
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Full document | emd_8215_full_validation.pdf.gz | 372 KB | Display | |
Data in XML | emd_8215_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | emd_8215_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8215 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8215 | HTTPS FTP |
-Related structure data
Related structure data | 5k7lMC M: atomic model generated by this map C: citing same article (ref.) |
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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_8215.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Voltage-gated K+ channel Eag1 bound to the channel...
File | emd_8215_additional_1.map | ||||||||||||
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Annotation | Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Voltage-gated K+ channel Eag1 bound to the channel...
File | emd_8215_additional_2.map | ||||||||||||
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Annotation | Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Voltage-gated K+ channel Eag1 bound to the channel...
File | emd_8215_additional_3.map | ||||||||||||
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Annotation | Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Voltage-gated K+ channel Eag1 bound to the channel inhibitor calm...
Entire | Name: Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin |
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Components |
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-Supramolecule #1: Voltage-gated K+ channel Eag1 bound to the channel inhibitor calm...
Supramolecule | Name: Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 450 KDa |
-Supramolecule #2: Voltage-gated potassium channel Eag1
Supramolecule | Name: Voltage-gated potassium channel Eag1 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) / Location in cell: Cell membrane |
Molecular weight | Theoretical: 380 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293 GnTI- / Recombinant plasmid: pEG BacMam |
-Supramolecule #3: Calmodulin
Supramolecule | Name: Calmodulin / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293 GnTI- / Recombinant plasmid: pEG BacMam |
-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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 97.359766 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTMAGGRRGL VAPQNTFLEN IVRRSNDTNF VLGNAQIVDW PIVYSNDGFC KLSGYHRAEV MQKSSACSFM YGELTDKDTV EKVRQTFEN YEMNSFEILM YKKNRTPVWF FVKIAPIRNE QDKVVLFLCT FSDITAFKQP IEDDSCKGWG KFARLTRALT S SRGVLQQL ...String: MTMAGGRRGL VAPQNTFLEN IVRRSNDTNF VLGNAQIVDW PIVYSNDGFC KLSGYHRAEV MQKSSACSFM YGELTDKDTV EKVRQTFEN YEMNSFEILM YKKNRTPVWF FVKIAPIRNE QDKVVLFLCT FSDITAFKQP IEDDSCKGWG KFARLTRALT S SRGVLQQL APSVQKGENV HKHSRLAEVL QLGSDILPQY KQEAPKTPPH IILHYCVFKT TWDWIILILT FYTAILVPYN VS FKTRQNN VAWLVVDSIV DVIFLVDIVL NFHTTFVGPA GEVISDPKLI RMNYLKTWFV IDLLSCLPYD VINAFENVDE GIS SLFSSL KVVRLLRLGR VARKLDHYIE YGAAVLVLLV CVFGLAAHWM ACIWYSIGDY EIFDEDTKTI RNNSWLYQLA LDIG TPYQF NGSGSGKWEG GPSKNSVYIS SLYFTMTSLT SVGFGNIAPS TDIEKIFAVA IMMIGSLLYA TIFGNVTTIF QQMYA NTNR YHEMLNSVRD FLKLYQVPKG LSERVMDYIV STWSMSRGID TEKVLQICPK DMRADICVHL NRKVFKEHPA FRLASD GCL RALAMEFQTV HCAPGDLIYH AGESVDSLCF VVSGSLEVIQ DDEVVAILGK GDVFGDVFWK EATLAQSCAN VRALTYC DL HVIKRDALQK VLEFYTAFSH SFSRNLILTY NLRKRIVFRK ISDVKREEEE RMKRKNEAPL ILPPDHPVRR LFQRFRQQ K EARLAAERGG RDLDDLDVEK GNALTDHTSA NHSLVKASVV TVRESPATPV SFYPIPEQTL QATVLEVKHE LKEDIKALN AKMTSIEKQL SEILRILMSR GSSQSPQDTC EVSRPQSPES DRDIFGASSN SLEVLFQ |
-Macromolecule #2: Calmodulin
Macromolecule | Name: Calmodulin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.852545 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 86 % / Instrument: FEI VITROBOT MARK IV Details: Plunged into liquid ethane (FEI VITROBOT MARK IV). |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1657 / Average electron dose: 1.8 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: 3.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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Output model | PDB-5k7l: |