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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
Keywordsvoltage-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
Potassium channel, voltage-dependent, EAG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / : ...Potassium channel, voltage-dependent, EAG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / 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 / Voltage-gated delayed rectifier potassium channel KCNH1
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-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing 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)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å
1.08 Å/pix.
x 256 pix.
= 276.48 Å
1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

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

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Half map: #1

Fileemd_28487_half_map_1.map
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Half map: #2

Fileemd_28487_half_map_2.map
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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 / 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

UniProtKB: Voltage-gated delayed rectifier potassium channel KCNH1

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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

UniProtKB: Calmodulin-1

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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 / Pretreatment - Time: 22 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: OTHER
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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