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- EMDB-32494: C1 map of TM domain of human Kv1.3 channel in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-32494
TitleC1 map of TM domain of human Kv1.3 channel in apo state
Map data
Sample
  • Complex: C1 map of TM domain of human Kv1.3 channel in apo state
    • Complex: TM domain focused map of human Kv1.3 channel bound to dalazatide
    • Complex: Focused map of human Kv1.3 channel T1 domains and beta 2.1 subunits
Function / homology
Function and homology information


voltage-gated monoatomic ion channel activity / corpus callosum development / delayed rectifier potassium channel activity / Voltage gated Potassium channels / outward rectifier potassium channel activity / optic nerve development / action potential / calyx of Held / voltage-gated potassium channel activity / voltage-gated potassium channel complex ...voltage-gated monoatomic ion channel activity / corpus callosum development / delayed rectifier potassium channel activity / Voltage gated Potassium channels / outward rectifier potassium channel activity / optic nerve development / action potential / calyx of Held / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / potassium ion transport / protein homooligomerization / presynaptic membrane / postsynaptic membrane / membrane raft / axon / glutamatergic synapse / perinuclear region of cytoplasm / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily A member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsTyagi A / Ahmed T / Jian S / Bajaj S / Ong ST / Goay SSM / Zhao Y / Vorobyov I / Tian C / Chandy KG / Bhushan S
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2017-T2-2-089, MOE2020-T1-002-059, MOE2016-T2-2-032 Singapore
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Rearrangement of a unique Kv1.3 selectivity filter conformation upon binding of a drug.
Authors: Anu Tyagi / Tofayel Ahmed / Shi Jian / Saumya Bajaj / Seow Theng Ong / Stephanie Shee Min Goay / Yue Zhao / Igor Vorobyov / Changlin Tian / K George Chandy / Shashi Bhushan /
Abstract: We report two structures of the human voltage-gated potassium channel (Kv) Kv1.3 in immune cells alone (apo-Kv1.3) and bound to an immunomodulatory drug called dalazatide (dalazatide-Kv1.3). Both the ...We report two structures of the human voltage-gated potassium channel (Kv) Kv1.3 in immune cells alone (apo-Kv1.3) and bound to an immunomodulatory drug called dalazatide (dalazatide-Kv1.3). Both the apo-Kv1.3 and dalazatide-Kv1.3 structures are in an activated state based on their depolarized voltage sensor and open inner gate. In apo-Kv1.3, the aromatic residue in the signature sequence (Y447) adopts a position that diverges 11 Å from other K channels. The outer pore is significantly rearranged, causing widening of the selectivity filter and perturbation of ion binding within the filter. This conformation is stabilized by a network of intrasubunit hydrogen bonds. In dalazatide-Kv1.3, binding of dalazatide to the channel's outer vestibule narrows the selectivity filter, Y447 occupies a position seen in other K channels, and this conformation is stabilized by a network of intersubunit hydrogen bonds. These remarkable rearrangements in the selectivity filter underlie Kv1.3's transition into the drug-blocked state.
History
DepositionDec 29, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateAug 24, 2022-
Current statusAug 24, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32494.png

Downloads & links

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Map

FileDownload / File: emd_32494.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 257.4 Å		0.86 Å/pix.
x 300 pix.
= 257.4 Å		0.86 Å/pix.
x 300 pix.
= 257.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.858 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.052625366 - 0.08836777
Average (Standard dev.)9.1720605e-05 (±0.0015077341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 257.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8580.8580.858
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z257.400257.400257.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0530.0880.000

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Supplemental data

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Sample components

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Entire : C1 map of TM domain of human Kv1.3 channel in apo state

EntireName: C1 map of TM domain of human Kv1.3 channel in apo state
Components
  • Complex: C1 map of TM domain of human Kv1.3 channel in apo state
    • Complex: TM domain focused map of human Kv1.3 channel bound to dalazatide
    • Complex: Focused map of human Kv1.3 channel T1 domains and beta 2.1 subunits

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Supramolecule #1: C1 map of TM domain of human Kv1.3 channel in apo state

SupramoleculeName: C1 map of TM domain of human Kv1.3 channel in apo state
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera (butterflies/moths)

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Supramolecule #2: TM domain focused map of human Kv1.3 channel bound to dalazatide

SupramoleculeName: TM domain focused map of human Kv1.3 channel bound to dalazatide
type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera (butterflies/moths)

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Supramolecule #3: Focused map of human Kv1.3 channel T1 domains and beta 2.1 subunits

SupramoleculeName: Focused map of human Kv1.3 channel T1 domains and beta 2.1 subunits
type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #1, #3

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 177130
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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