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- EMDB-32459: Composite map of human Kv1.3 channel in apo state with beta subunits -

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Basic information

Entry
Database: EMDB / ID: EMD-32459
TitleComposite map of human Kv1.3 channel in apo state with beta subunits
Map dataComposite map of human Kv1.3 channel with beta subunits
Sample
  • Complex: Composite map of human Kv1.3 channel in apo state with beta subunits
    • Complex: TM domain focused map of human Kv1.3
      • Protein or peptide: Potassium voltage-gated channel subfamily A member 3
    • Complex: Soluble domain focused map of human Kv1.3
      • Protein or peptide: Potassium voltage-gated channel subfamily A member 3
      • Protein or peptide: Voltage-gated potassium channel subunit beta-2
  • Ligand: POTASSIUM ION
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • 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 / delayed rectifier potassium channel activity / aldo-keto reductase (NADPH) 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 / delayed rectifier potassium channel activity / aldo-keto reductase (NADPH) activity / Voltage gated Potassium channels / juxtaparanode region of axon / outward rectifier potassium channel activity / 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 / voltage-gated potassium channel activity / potassium channel regulator activity / specific granule membrane / voltage-gated potassium channel complex / calyx of Held / 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 / synapse / Neutrophil degranulation / perinuclear region of cytoplasm / glutamatergic synapse / 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 / Voltage-gated potassium channel / NADP-dependent oxidoreductase domain ...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 / Voltage-gated potassium channel / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / Voltage-dependent channel domain superfamily / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7wf3
  • Surface level: 6.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32459.png

Downloads & links

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Map

FileDownload / File: emd_32459.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of human Kv1.3 channel with beta subunits
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: 6.0 / Movie #1: 6.5
Minimum - Maximum-39.824333000000003 - 65.093863999999996
Average (Standard dev.)-0.040874954 (±1.2148038)
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-39.82465.094-0.041

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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 apo state with beta subunits

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

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Supramolecule #1: Composite map of human Kv1.3 channel in apo state with beta subunits

SupramoleculeName: Composite map of human Kv1.3 channel in apo state with beta subunits
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: TM domain focused map of human Kv1.3

SupramoleculeName: TM domain focused map of human Kv1.3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Soluble domain focused map of human Kv1.3

SupramoleculeName: Soluble domain focused map of human Kv1.3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
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: 31.747734 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 YFYHRETEG

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: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #5: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 5 / 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 #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 116 / 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
Details: The above mentioned 3.4 Ang resolution was obtained for TM domain after application of C4 symmetry. The soluble domain map (another map deposited here) was resolved to 2.9 Ang.
Number images used: 177130
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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