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- EMDB-32460: Composite map of human Kv1.3 channel in dalazatide-bound state wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-32460
TitleComposite map of human Kv1.3 channel in dalazatide-bound state with beta subunits
Map dataComposite map generated by combining maps from focused refinement of TM and soluble domains
Sample
  • Complex: Composite map of human Kv1.3 channel in dalazatide-bound state with beta subunits
    • Complex: TM domain focused map of human Kv1.3 channel bound to dalazatide
      • Protein or peptide: Voltage-gated potassium channel subunit beta-2
    • Complex: Focused map of human Kv1.3 channel T1 domains and beta 2.1 subunits
      • Protein or peptide: Potassium voltage-gated channel subfamily A member 3
      • Protein or peptide: Potassium voltage-gated channel subfamily A member 3
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: POTASSIUM ION
  • Ligand: water
KeywordsIon channel / Kv channel / Potassium channel / Peptide toxin / ShK / Dalazatide / Selectivity filter / Molecular dynamics simulation / MEMBRANE PROTEIN
Function / homology
Function and homology information


pinceau fiber / regulation of action potential / methylglyoxal reductase (NADPH) (acetol producing) activity / NADPH oxidation / voltage-gated monoatomic ion channel activity / regulation of protein localization to cell surface / corpus callosum development / aldo-keto reductase (NADPH) activity / delayed rectifier potassium channel activity / Voltage gated Potassium channels ...pinceau fiber / regulation of action potential / methylglyoxal reductase (NADPH) (acetol producing) activity / NADPH oxidation / voltage-gated monoatomic ion channel activity / regulation of protein localization to cell surface / corpus callosum development / aldo-keto reductase (NADPH) activity / delayed rectifier potassium channel activity / Voltage gated Potassium channels / outward rectifier potassium channel activity / juxtaparanode region of axon / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / regulation of potassium ion transmembrane transport / optic nerve development / action potential / tertiary granule membrane / calyx of Held / voltage-gated potassium channel activity / potassium channel regulator activity / specific granule membrane / voltage-gated potassium channel complex / potassium ion transmembrane transport / potassium ion transport / protein homooligomerization / cytoplasmic side of plasma membrane / presynaptic membrane / postsynaptic membrane / transmembrane transporter binding / cytoskeleton / membrane raft / axon / glutamatergic synapse / Neutrophil degranulation / synapse / perinuclear region of cytoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family ...Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / 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 / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTyagi A / Ahmed T
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 25, 2021-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 9
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7wf4
  • Surface level: 9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32460.png

Downloads & links

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Map

FileDownload / File: emd_32460.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map generated by combining maps from focused refinement of TM and soluble domains
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 420 pix.
= 360.36 Å		0.86 Å/pix.
x 420 pix.
= 360.36 Å		0.86 Å/pix.
x 420 pix.
= 360.36 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: 9.0 / Movie #1: 9
Minimum - Maximum-55.984397999999999 - 103.628264999999999
Average (Standard dev.)0.014526618 (±1.3476912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 360.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8580.8580.858
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z360.360360.360360.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ420420420
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-55.984103.6280.015

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Supplemental data

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Sample components

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Entire : Composite map of human Kv1.3 channel in dalazatide-bound state wi...

EntireName: Composite map of human Kv1.3 channel in dalazatide-bound state with beta subunits
Components
  • Complex: Composite map of human Kv1.3 channel in dalazatide-bound state with beta subunits
    • Complex: TM domain focused map of human Kv1.3 channel bound to dalazatide
      • Protein or peptide: Voltage-gated potassium channel subunit beta-2
    • Complex: Focused map of human Kv1.3 channel T1 domains and beta 2.1 subunits
      • Protein or peptide: Potassium voltage-gated channel subfamily A member 3
      • Protein or peptide: Potassium voltage-gated channel subfamily A member 3
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: Composite map of human Kv1.3 channel in dalazatide-bound state wi...

SupramoleculeName: Composite map of human Kv1.3 channel in dalazatide-bound state with beta subunits
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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 / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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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 / ID: 3 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium voltage-gated channel subfamily A member 3

MacromoleculeName: Potassium voltage-gated channel subfamily A member 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.460467 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ERPLPRRDFQ RQVWLLFEYP ESSGPARGIA IVSVLVILIS IVIFCLETLP EFRDEKDYPA STSQDSFEAA GNSTSGSRAG ASSFSDPFF VVETLCIIWF SFELLVRFFA CPSKATFSRN IMNLIDIVAI IPYFITLGTE LAERQGNGQQ AMSLAILRVI R LVRVFRIF ...String:
ERPLPRRDFQ RQVWLLFEYP ESSGPARGIA IVSVLVILIS IVIFCLETLP EFRDEKDYPA STSQDSFEAA GNSTSGSRAG ASSFSDPFF VVETLCIIWF SFELLVRFFA CPSKATFSRN IMNLIDIVAI IPYFITLGTE LAERQGNGQQ AMSLAILRVI R LVRVFRIF KLSRHSKGLQ ILGQTLKASM RELGLLIFFL FIGVILFSSA VYFAEADDPT SGFSSIPDAF WWAVVTMTTV GY GDMHPVT IGGKIVGSLC AIAGVLTIAL PVPVIVSNFN YFYHRE

UniProtKB: Potassium voltage-gated channel subfamily A member 3

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Macromolecule #2: Voltage-gated potassium channel subunit beta-2

MacromoleculeName: Voltage-gated potassium channel subunit beta-2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.704254 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: RQLQFYRNLG KSGLRVSCLG LGTWVTFGGQ ITDEMAEQLM TLAYDNGINL FDTAEVYAAG KAEVVLGNII KKKGWRRSSL VITTKIFWG GKAETERGLS RKHIIEGLKA SLERLQLEYV DVVFANRPDP NTPMEETVRA MTHVINQGMA MYWGTSRWSS M EIMEAYSV ...String:
RQLQFYRNLG KSGLRVSCLG LGTWVTFGGQ ITDEMAEQLM TLAYDNGINL FDTAEVYAAG KAEVVLGNII KKKGWRRSSL VITTKIFWG GKAETERGLS RKHIIEGLKA SLERLQLEYV DVVFANRPDP NTPMEETVRA MTHVINQGMA MYWGTSRWSS M EIMEAYSV ARQFNLTPPI CEQAEYHMFQ REKVEVQLPE LFHKIGVGAM TWSPLACGIV SGKYDSGIPP YSRASLKGYQ WL KDKILSE EGRRQQAKLK ELQAIAERLG CTLPQLAIAW CLRNEGVSSV LLGASNADQL MENIGAIQVL PKLSSSIIHE IDS ILGNKP YS

UniProtKB: Voltage-gated potassium channel subunit beta-2

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Macromolecule #3: Potassium voltage-gated channel subfamily A member 3

MacromoleculeName: Potassium voltage-gated channel subfamily A member 3 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.777475 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
QDCCGERVVI NISGLRFETQ LKTLCQFPET LLGDPKRRMR YFDPLRNEYF FDRNRPSFDA ILYYYQSGGR IRRPVNVPID IFSEEIRFY QLGEEAMEKF REDEGFL

UniProtKB: Potassium voltage-gated channel subfamily A member 3

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Macromolecule #4: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 100 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153218
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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