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- EMDB-31148: human voltage-gated potassium channel KV1.3 -

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Basic information

Entry
Database: EMDB / ID: EMD-31148
Titlehuman voltage-gated potassium channel KV1.3
Map data
Sample
  • Complex: Human potassium channel KV1.3/KVb2.1 complex
    • Protein or peptide: Voltage-gated potassium channel subunit beta-2
    • Protein or peptide: Potassium voltage-gated channel subfamily A member 3
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Keywordspotassium channel / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / regulation of protein localization to cell surface / voltage-gated monoatomic ion channel activity / : / delayed rectifier potassium channel activity / Voltage gated Potassium channels / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / regulation of potassium ion transmembrane transport ...pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / regulation of protein localization to cell surface / voltage-gated monoatomic ion channel activity / : / delayed rectifier potassium channel activity / Voltage gated Potassium channels / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / regulation of potassium ion transmembrane transport / tertiary granule membrane / action potential / voltage-gated potassium channel activity / potassium channel regulator activity / specific granule membrane / voltage-gated potassium channel complex / potassium ion transmembrane transport / protein homooligomerization / potassium ion transport / cytoplasmic side of plasma membrane / transmembrane transporter binding / cytoskeleton / axon / synapse / Neutrophil degranulation / 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 / 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 / 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: 3.2 Å
AuthorsLiu S / Zhao Y
CitationJournal: Cell Discov / Year: 2021
Title: Structures of wild-type and H451N mutant human lymphocyte potassium channel K1.3.
Authors: Sanling Liu / Yue Zhao / Hao Dong / Liang Xiao / Yong Zhang / Yuqin Yang / Seow Theng Ong / K George Chandy / Longhua Zhang / Changlin Tian /
History
DepositionApr 1, 2021-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ej1
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31148.png

Downloads & links

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Map

FileDownload / File: emd_31148.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.)
1.01 Å/pix.
x 300 pix.
= 304.2 Å		1.01 Å/pix.
x 300 pix.
= 304.2 Å		1.01 Å/pix.
x 300 pix.
= 304.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.01
Minimum - Maximum-0.051006198 - 0.11066485
Average (Standard dev.)0.00014040941 (±0.0022564735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 304.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z304.200304.200304.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-288-288-288
NX/NY/NZ576576576
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0510.1110.000

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Supplemental data

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Sample components

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Entire : Human potassium channel KV1.3/KVb2.1 complex

EntireName: Human potassium channel KV1.3/KVb2.1 complex
Components
  • Complex: Human potassium channel KV1.3/KVb2.1 complex
    • Protein or peptide: Voltage-gated potassium channel subunit beta-2
    • Protein or peptide: Potassium voltage-gated channel subfamily A member 3
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: Human potassium channel KV1.3/KVb2.1 complex

SupramoleculeName: Human potassium channel KV1.3/KVb2.1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Voltage-gated potassium channel subunit beta-2

MacromoleculeName: Voltage-gated potassium channel subunit beta-2 / type: protein_or_peptide / ID: 1 / 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: 41.049152 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MYPESTTGSP ARLSLRQTGS PGMIYSTRYG SPKRQLQFYR NLGKSGLRVS CLGLGTWVTF GGQITDEMAE QLMTLAYDNG INLFDTAEV YAAGKAEVVL GNIIKKKGWR RSSLVITTKI FWGGKAETER GLSRKHIIEG LKASLERLQL EYVDVVFANR P DPNTPMEE ...String:
MYPESTTGSP ARLSLRQTGS PGMIYSTRYG SPKRQLQFYR NLGKSGLRVS CLGLGTWVTF GGQITDEMAE QLMTLAYDNG INLFDTAEV YAAGKAEVVL GNIIKKKGWR RSSLVITTKI FWGGKAETER GLSRKHIIEG LKASLERLQL EYVDVVFANR P DPNTPMEE TVRAMTHVIN QGMAMYWGTS RWSSMEIMEA YSVARQFNLT PPICEQAEYH MFQREKVEVQ LPELFHKIGV GA MTWSPLA CGIVSGKYDS GIPPYSRASL KGYQWLKDKI LSEEGRRQQA KLKELQAIAE RLGCTLPQLA IAWCLRNEGV SSV LLGASN ADQLMENIGA IQVLPKLSSS IIHEIDSILG NKPYSKKDYR S

UniProtKB: Voltage-gated potassium channel subunit beta-2

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Macromolecule #2: Potassium voltage-gated channel subfamily A member 3

MacromoleculeName: Potassium voltage-gated channel subfamily A member 3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.90648 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDERLSLLRS PPPPSARHRA HPPQRPASSG GAHTLVNHGY AEPAAGRELP PDMTVVPGDH LLEPEVADGG GAPPQGGCGG GGCDRYEPL PPSLPAAGEQ DCCGERVVIN ISGLRFETQL KTLCQFPETL LGDPKRRMRY FDPLRNEYFF DRNRPSFDAI L YYYQSGGR ...String:
MDERLSLLRS PPPPSARHRA HPPQRPASSG GAHTLVNHGY AEPAAGRELP PDMTVVPGDH LLEPEVADGG GAPPQGGCGG GGCDRYEPL PPSLPAAGEQ DCCGERVVIN ISGLRFETQL KTLCQFPETL LGDPKRRMRY FDPLRNEYFF DRNRPSFDAI L YYYQSGGR IRRPVNVPID IFSEEIRFYQ LGEEAMEKFR EDEGFLREEE RPLPRRDFQR QVWLLFEYPE SSGPARGIAI VS VLVILIS IVIFCLETLP EFRDEKDYPA STSQDSFEAA GNSTSGSRAG ASSFSDPFFV VETLCIIWFS FELLVRFFAC PSK ATFSRN IMNLIDIVAI IPYFITLGTE LAERQGNGQQ AMSLAILRVI RLVRVFRIFK LSRHSKGLQI LGQTLKASMR ELGL LIFFL FIGVILFSSA VYFAEADDPT SGFSSIPDAF WWAVVTMTTV GYGDMHPVTI GGKIVGSLCA IAGVLTIALP VPVIV SNFN YFYHRETEGE EQSQYMHVGS CQHLSSSAEE LRKARSNSTL SKSEYMVIEE GGMNHSAFPQ TPFKTGNSTA TCTTNN NPN SCVNIKKIFT DV

UniProtKB: Potassium voltage-gated channel subfamily A member 3

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Macromolecule #3: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: 3.2 Å / Number images used: 44078
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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