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- EMDB-49993: Kv2.1 with voltage sensor in the up conformation under high potassium -

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Basic information

Entry
Database: EMDB / ID: EMD-49993
TitleKv2.1 with voltage sensor in the up conformation under high potassium
Map data
Sample
  • Cell: human Kv2.1
    • Protein or peptide: Potassium voltage-gated channel subfamily B member 1
Keywordsvoltage-gated potassium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of action potential / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / cholinergic synapse / potassium ion export across plasma membrane / positive regulation of calcium ion-dependent exocytosis / delayed rectifier potassium channel activity ...regulation of action potential / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / cholinergic synapse / potassium ion export across plasma membrane / positive regulation of calcium ion-dependent exocytosis / delayed rectifier potassium channel activity / proximal dendrite / Voltage gated Potassium channels / outward rectifier potassium channel activity / vesicle docking involved in exocytosis / response to L-glutamate / glutamate receptor signaling pathway / postsynaptic specialization membrane / neuronal cell body membrane / action potential / lateral plasma membrane / positive regulation of protein targeting to membrane / potassium channel regulator activity / response to axon injury / cellular response to nutrient levels / voltage-gated potassium channel complex / potassium ion transmembrane transport / dendrite membrane / cellular response to calcium ion / SNARE binding / protein localization to plasma membrane / cellular response to glucose stimulus / negative regulation of insulin secretion / sarcolemma / protein homooligomerization / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / glucose homeostasis / perikaryon / transmembrane transporter binding / postsynaptic membrane / apical plasma membrane / protein heterodimerization activity / axon / dendrite / perinuclear region of cytoplasm / cell surface / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv2.1 / Potassium channel, voltage dependent, Kv2 / Kv2 voltage-gated K+ channel / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / Voltage-dependent channel domain superfamily / BTB/POZ domain ...Potassium channel, voltage dependent, Kv2.1 / Potassium channel, voltage dependent, Kv2 / Kv2 voltage-gated K+ channel / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / Voltage-dependent channel domain superfamily / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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: 2025
Title: Electric field-induced pore constriction in the human K2.1 channel.
Authors: Venkata Shiva Mandala / Roderick MacKinnon /
Abstract: Gating in voltage-dependent ion channels is regulated by the transmembrane voltage. This form of regulation is enabled by voltage-sensing domains (VSDs) that respond to transmembrane voltage ...Gating in voltage-dependent ion channels is regulated by the transmembrane voltage. This form of regulation is enabled by voltage-sensing domains (VSDs) that respond to transmembrane voltage differences by changing their conformation and exerting force on the pore to open or close it. Here, we use cryogenic electron microscopy to study the neuronal K2.1 channel in lipid vesicles with and without a voltage difference across the membrane. Hyperpolarizing voltage differences displace the positively charged S4 helix in the voltage sensor by one helical turn (~5 Å). When this displacement occurs, the S4 helix changes its contact with the pore at two different interfaces. When these changes are observed in fewer than four voltage sensors, the pore remains open, but when they are observed in all four voltage sensors, the pore constricts. The constriction occurs because the S4 helix, as it displaces inward, squeezes the right-handed helical bundle of pore-lining S6 helices. A similar conformational change occurs upon hyperpolarization of the EAG1 channel but with two helical turns displaced instead of one. Therefore, while K2.1 and EAG1 are from distinct architectural classes of voltage-dependent ion channels, called domain-swapped and non-domain-swapped, the way the voltage sensors gate their pores is very similar.
History
DepositionApr 3, 2025-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49993.png

Downloads & links

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Map

FileDownload / File: emd_49993.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 216.064 Å		0.84 Å/pix.
x 256 pix.
= 216.064 Å		0.84 Å/pix.
x 256 pix.
= 216.064 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.24821883 - 0.48814717
Average (Standard dev.)0.003152119 (±0.02106075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.064 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_49993_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_49993_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49993_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : human Kv2.1

EntireName: human Kv2.1
Components
  • Cell: human Kv2.1
    • Protein or peptide: Potassium voltage-gated channel subfamily B member 1

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Supramolecule #1: human Kv2.1

SupramoleculeName: human Kv2.1 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Potassium voltage-gated channel subfamily B member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.001711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPAGMTKHGS RSTSSLPPEP MEIVRSKACS RRVRLNVGGL AHEVLWRTLD RLPRTRLGKL RDCNTHDSLL EVCDDYSLDD NEYFFDRHP GAFTSILNFY RTGRLHMMEE MCALSFSQEL DYWGIDEIYL ESCCQARYHQ KKEQMNEELK REAETLRERE G EEFDNTCC ...String:
MPAGMTKHGS RSTSSLPPEP MEIVRSKACS RRVRLNVGGL AHEVLWRTLD RLPRTRLGKL RDCNTHDSLL EVCDDYSLDD NEYFFDRHP GAFTSILNFY RTGRLHMMEE MCALSFSQEL DYWGIDEIYL ESCCQARYHQ KKEQMNEELK REAETLRERE G EEFDNTCC AEKRKKLWDL LEKPNSSVAA KILAIISIMF IVLSTIALSL NTLPELQSLD EFGQSTDNPQ LAHVEAVCIA WF TMEYLLR FLSSPKKWKF FKGPLNAIDL LAILPYYVTI FLTESNKSVL QFQNVRRVVQ IFRIMRILRI LKLARHSTGL QSL GFTLRR SYNELGLLIL FLAMGIMIFS SLVFFAEKDE DDTKFKSIPA SFWWATITMT TVGYGDIYPK TLLGKIVGGL CCIA GVLVI ALPIPIIVNN FSEFYKEQKR QEKAIKRREA LERAKRNGSI VSMNMKDAFA RSIEMMDIVV EKNGENMGKK DKVQD NHLS PNKWKWTKRT LSETSSSKSF ETKEQGSPEK ARSSSSPQHL NVQQLEDMYN KMAKTQSQPI LNTKESAAQS KPKEEL EME SIPSPVAPLP TRTEGVIDMR SMSSIDSFIS CATDFPEATR FSHSPLTSLP SKTGGSTAPE VGWRGALGAS GGRFVEA NP SPDASQHSSF FIESPKSSMK TNNPLKLRAL KVNFMEGDPS PLLPVLGMYH DPLRNRGSAA AAVAGLECAT LLDKAVLS P ESSIYTTASA KTPPRSPEKH TAIAFNFEAG VHQYIDADTD DEGQLLYSVD SSPPKSLPGS TSPKFSTGTR SEKNHFESS PLPTSPKFLR QNCIYSTEAL TGKGPSGQEK CKLENHISPD VRVLPGGGAH GSTRDQSI

UniProtKB: Potassium voltage-gated channel subfamily B member 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65670
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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