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- EMDB-31013: CryoEM structure of human Kv4.2-DPP6S complex -

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Basic information

Entry
Database: EMDB / ID: EMD-31013
TitleCryoEM structure of human Kv4.2-DPP6S complex
Map datamap E
Sample
  • Cell: human Kv4.2-DPP6S complex
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6
    • Protein or peptide: Potassium voltage-gated channel subfamily D member 2
    • Protein or peptide: Potassium voltage-gated channel subfamily D member 2
Keywordsmembrane protein
Function / homology
Function and homology information


Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / anchoring junction / postsynaptic specialization membrane / neuronal cell body membrane ...Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / anchoring junction / postsynaptic specialization membrane / neuronal cell body membrane / regulation of heart contraction / locomotor rhythm / action potential / plasma membrane raft / voltage-gated potassium channel activity / potassium channel regulator activity / neuronal action potential / voltage-gated potassium channel complex / potassium ion transmembrane transport / sensory perception of pain / serine-type peptidase activity / muscle contraction / protein localization to plasma membrane / protein homooligomerization / GABA-ergic synapse / perikaryon / cellular response to hypoxia / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuronal cell body / glutamatergic synapse / proteolysis / metal ion binding / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv4.2 / Potassium channel, voltage dependent, Kv4 / Potassium channel, voltage dependent, Kv4, C-terminal / Domain of unknown function (DUF3399) / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / : ...Potassium channel, voltage dependent, Kv4.2 / Potassium channel, voltage dependent, Kv4 / Potassium channel, voltage dependent, Kv4, C-terminal / Domain of unknown function (DUF3399) / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Voltage-gated potassium channel / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
A-type potassium channel modulatory protein DPP6 / A-type voltage-gated potassium channel KCND2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKise Y / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nature / Year: 2021
Title: Structural basis of gating modulation of Kv4 channel complexes.
Authors: Yoshiaki Kise / Go Kasuya / Hiroyuki H Okamoto / Daichi Yamanouchi / Kan Kobayashi / Tsukasa Kusakizako / Tomohiro Nishizawa / Koichi Nakajo / Osamu Nureki /
Abstract: Modulation of voltage-gated potassium (Kv) channels by auxiliary subunits is central to the physiological function of channels in the brain and heart. Native Kv4 tetrameric channels form ...Modulation of voltage-gated potassium (Kv) channels by auxiliary subunits is central to the physiological function of channels in the brain and heart. Native Kv4 tetrameric channels form macromolecular ternary complexes with two auxiliary β-subunits-intracellular Kv channel-interacting proteins (KChIPs) and transmembrane dipeptidyl peptidase-related proteins (DPPs)-to evoke rapidly activating and inactivating A-type currents, which prevent the backpropagation of action potentials. However, the modulatory mechanisms of Kv4 channel complexes remain largely unknown. Here we report cryo-electron microscopy structures of the Kv4.2-DPP6S-KChIP1 dodecamer complex, the Kv4.2-KChIP1 and Kv4.2-DPP6S octamer complexes, and Kv4.2 alone. The structure of the Kv4.2-KChIP1 complex reveals that the intracellular N terminus of Kv4.2 interacts with its C terminus that extends from the S6 gating helix of the neighbouring Kv4.2 subunit. KChIP1 captures both the N and the C terminus of Kv4.2. In consequence, KChIP1 would prevent N-type inactivation and stabilize the S6 conformation to modulate gating of the S6 helices within the tetramer. By contrast, unlike the reported auxiliary subunits of voltage-gated channel complexes, DPP6S interacts with the S1 and S2 helices of the Kv4.2 voltage-sensing domain, which suggests that DPP6S stabilizes the conformation of the S1-S2 helices. DPP6S may therefore accelerate the voltage-dependent movement of the S4 helices. KChIP1 and DPP6S do not directly interact with each other in the Kv4.2-KChIP1-DPP6S ternary complex. Thus, our data suggest that two distinct modes of modulation contribute in an additive manner to evoke A-type currents from the native Kv4 macromolecular complex.
History
DepositionMar 1, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing 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
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7e8b
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7e8b
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31013.png

Downloads & links

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Map

FileDownload / File: emd_31013.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap E
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 332 pix.
= 332. Å		1 Å/pix.
x 332 pix.
= 332. Å		1 Å/pix.
x 332 pix.
= 332. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.043739304 - 0.091944315
Average (Standard dev.)0.00032865084 (±0.002437122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions332332332
Spacing332332332
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z332332332
origin x/y/z0.0000.0000.000
length x/y/z332.000332.000332.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS332332332
D min/max/mean-0.0440.0920.000

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Supplemental data

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Mask #1

Fileemd_31013_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_31013_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_31013_half_map_2.map
Projections & Slices
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Sample components

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Entire : human Kv4.2-DPP6S complex

EntireName: human Kv4.2-DPP6S complex
Components
  • Cell: human Kv4.2-DPP6S complex
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6
    • Protein or peptide: Potassium voltage-gated channel subfamily D member 2
    • Protein or peptide: Potassium voltage-gated channel subfamily D member 2

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Supramolecule #1: human Kv4.2-DPP6S complex

SupramoleculeName: human Kv4.2-DPP6S complex / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Dipeptidyl aminopeptidase-like protein 6

MacromoleculeName: Dipeptidyl aminopeptidase-like protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.392797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WKGIAIALLV ILVICSLIVT SVILLTPAED NSLSQKKKVT VEDLFSEDFK IHDPEAKWIS DTEFIYREQK GTVRLWNVET NTSTVLIEG KKIESLRAIR YEISPDREYA LFSYNVEPIY QHSYTGYYVL SKIPHGDPQS LDPPEVSNAK LQYAGWGPKG Q QLIFIFEN ...String:
WKGIAIALLV ILVICSLIVT SVILLTPAED NSLSQKKKVT VEDLFSEDFK IHDPEAKWIS DTEFIYREQK GTVRLWNVET NTSTVLIEG KKIESLRAIR YEISPDREYA LFSYNVEPIY QHSYTGYYVL SKIPHGDPQS LDPPEVSNAK LQYAGWGPKG Q QLIFIFEN NIYYCAHVGK QAIRVVSTGK EGVIYNGLSD WLYEEEILKT HIAHWWSPDG TRLAYAAIND SRVPIMELPT YT GSIYPTV KPYHYPKAGS ENPSISLHVI GLNGPTHDLE MMPPDDPRMR EYYITMVKWA TSTKVAVTWL NRAQNVSILT LCD ATTGVC TKKHEDESEA WLHRQNEEPV FSKDGRKFFF IRAIPQGGRG KFYHITVSSS QPNSSNDNIQ SITSGDWDVT KILA YDEKG NKIYFLSTED LPRRRQLYSA NTVGNFNRQC LSCDLVENCT YFSASFSHSM DFFLLKCEGP GVPMVTVHNT TDKKK MFDL ETNEHVKKAI NDRQMPKVEY RDIEIDDYNL PMQILKPATF TDTTHYPLLL VVDGTPGSQS VAEKFEVSWE TVMVSS HGA VVVKCDGRGS GFQGTKLLHE VRRRLGLLEE KDQMEAVRTM LKEQYIDRTR VAVFGKDYGG YLSTYILPAK GENQGQT FT CGSALSPITD FKLYASAFSE RYLGLHGLDN RAYEMTKVAH RVSALEEQQF LIIHPTADEK IHFQHTAELI TQLIRGKA N YSLQIYPDES HYFTSSSLKQ HLYRSIINFF VECFRI

UniProtKB: A-type potassium channel modulatory protein DPP6

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Macromolecule #2: Potassium voltage-gated channel subfamily D member 2

MacromoleculeName: Potassium voltage-gated channel subfamily D member 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.297133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DALIVLNVSG TRFQTWQDTL ERYPDTLLGS SERDFFYHPE TQQYFFDRDP DIFRHILNFY RTGKLHYPRH ECISAYDEEL AFFGLIPEI IGDCCYEEYK DRRRENAERL QDDADTDTAG ESALPTMTAR QRVWRAFENP HTSTMALVFY YVTGFFIAVS V IANVVETV ...String:
DALIVLNVSG TRFQTWQDTL ERYPDTLLGS SERDFFYHPE TQQYFFDRDP DIFRHILNFY RTGKLHYPRH ECISAYDEEL AFFGLIPEI IGDCCYEEYK DRRRENAERL QDDADTDTAG ESALPTMTAR QRVWRAFENP HTSTMALVFY YVTGFFIAVS V IANVVETV PCGSSPGHIK ELPCGERYAV AFFCLDTACV MIFTVEYLLR LAAAPSRYRF VRSVMSIIDV VAILPYYIGL VM TDNEDVS GAFVTLRVFR VFRIFKFSRH SQGLRILGYT LKSCASELGF LLFSLTMAII IFATVMFYAE KGSSASKFTS IPA AFWYTI VTMTTLGYGD MVPKTIAGKI FGSICSLSGV LVIALPVPVI VSNFSRIYHQ NQRADKRRAQ KKARLARIRA AK

UniProtKB: A-type voltage-gated potassium channel KCND2

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

MacromoleculeName: Potassium voltage-gated channel subfamily D member 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.167953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DALIVLNVSG TRFQTWQDTL ERYPDTLLGS SERDFFYHPE TQQYFFDRDP DIFRHILNFY RTGKLHYPRH ECISAYDEEL AFFGLIPEI IGDCCYEEYK DRRRENAERL QDDADTDTAG ESALPTMTAR QRVWRAFENP HTSTMALVFY YVTGFFIAVS V IANVVETV ...String:
DALIVLNVSG TRFQTWQDTL ERYPDTLLGS SERDFFYHPE TQQYFFDRDP DIFRHILNFY RTGKLHYPRH ECISAYDEEL AFFGLIPEI IGDCCYEEYK DRRRENAERL QDDADTDTAG ESALPTMTAR QRVWRAFENP HTSTMALVFY YVTGFFIAVS V IANVVETV PCGSSPGHIK ELPCGERYAV AFFCLDTACV MIFTVEYLLR LAAAPSRYRF VRSVMSIIDV VAILPYYIGL VM TDNEDVS GAFVTLRVFR VFRIFKFSRH SQGLRILGYT LKSCASELGF LLFSLTMAII IFATVMFYAE KGSSASKFTS IPA AFWYTI VTMTTLGYGD MVPKTIAGKI FGSICSLSGV LVIALPVPVI VSNFSRIYHQ NQRADKRRAQ KKARLARIRA A

UniProtKB: A-type voltage-gated potassium channel KCND2

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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91974
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7e8b:
CryoEM structure of human Kv4.2-DPP6S complex

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