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- EMDB-28487: Eag Kv channel with voltage sensor in the up conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-28487
TitleEag Kv channel with voltage sensor in the up conformation
Map data
Sample
  • Complex: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+
    • Protein or peptide: Potassium voltage-gated channel subfamily H member 1
    • Protein or peptide: Calmodulin-1
Function / homology
Function and homology information


Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / CaM pathway / parallel fiber to Purkinje cell synapse / Cam-PDE 1 activation / Sodium/Calcium exchangers / nuclear inner membrane ...Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / CaM pathway / parallel fiber to Purkinje cell synapse / 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 / phosphatidylinositol bisphosphate binding / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / startle response / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / axolemma / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / cellular response to calcium ion / substantia nigra development / adenylate cyclase activator activity / regulation of membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / monoatomic ion transmembrane transport / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / 14-3-3 protein binding / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / VEGFR2 mediated cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / postsynaptic density membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion
Similarity search - Function
Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Potassium voltage-gated channel subfamily H member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMandala VS / MacKinnon R
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionOct 4, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_28487.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.0250188 - 1.3934448
Average (Standard dev.)0.004256202 (±0.036186296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_28487_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_28487_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_28487_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+

EntireName: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+
Components
  • Complex: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+
    • Protein or peptide: Potassium voltage-gated channel subfamily H member 1
    • Protein or peptide: Calmodulin-1

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Supramolecule #1: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+

SupramoleculeName: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Potassium voltage-gated channel subfamily H member 1

MacromoleculeName: Potassium voltage-gated channel subfamily H member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 81.664094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.063608 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EEQIAEFKEA FSLFDKDGDG TITTKELGTV MRSLGQNPTE AELQDMINEV DADGNGTIDF PEFLTMMARK MKDTDSEEEI REAFRVFDK DGNGYISAAE LRHVMTNLGE KLTDEEVDEM IREADIDGDG QVNYEEFVQM MTA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49164
FSC plot (resolution estimation)

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