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- EMDB-31012: CryoEM structure of human Kv4.2-DPP6S complex, extracellular region -

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Basic information

Entry
Database: EMDB / ID: EMD-31012
TitleCryoEM structure of human Kv4.2-DPP6S complex, extracellular region
Map data
Sample
  • Complex: human Kv4.2-DPP6S complex
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6
Keywordsmembrane protein
Function / homology
Function and homology information


regulation of potassium ion transmembrane transport / potassium channel regulator activity / voltage-gated potassium channel complex / serine-type peptidase activity / protein localization to plasma membrane / proteolysis / membrane / plasma membrane
Similarity search - Function
: / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
A-type potassium channel modulatory protein DPP6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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: 0.0165
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0165
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  • Surface view with fitted model
  • Atomic models: PDB-7e89
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7e89
  • Imaged by Jmol
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Structure viewerEM map:
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Supplemental images

emd_31012.png

Downloads & links

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Map

FileDownload / File: emd_31012.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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: 0.0165 / Movie #1: 0.0165
Minimum - Maximum-0.037475724 - 0.092979364
Average (Standard dev.)0.00031757835 (±0.0023516973)
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-0.0370.0930.000

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Supplemental data

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Mask #1

Fileemd_31012_msk_1.map
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Half map: #1

Fileemd_31012_half_map_1.map
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Half map: #2

Fileemd_31012_half_map_2.map
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Sample components

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Entire : human Kv4.2-DPP6S complex

EntireName: human Kv4.2-DPP6S complex
Components
  • Complex: human Kv4.2-DPP6S complex
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6

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Supramolecule #1: human Kv4.2-DPP6S complex

SupramoleculeName: human Kv4.2-DPP6S complex / type: complex / 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: 83.476094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EDNSLSQKKK VTVEDLFSED FKIHDPEAKW ISDTEFIYRE QKGTVRLWNV ETNTSTVLIE GKKIESLRAI RYEISPDREY ALFSYNVEP IYQHSYTGYY VLSKIPHGDP QSLDPPEVSN AKLQYAGWGP KGQQLIFIFE NNIYYCAHVG KQAIRVVSTG K EGVIYNGL ...String:
EDNSLSQKKK VTVEDLFSED FKIHDPEAKW ISDTEFIYRE QKGTVRLWNV ETNTSTVLIE GKKIESLRAI RYEISPDREY ALFSYNVEP IYQHSYTGYY VLSKIPHGDP QSLDPPEVSN AKLQYAGWGP KGQQLIFIFE NNIYYCAHVG KQAIRVVSTG K EGVIYNGL SDWLYEEEIL KTHIAHWWSP DGTRLAYAAI NDSRVPIMEL PTYTGSIYPT VKPYHYPKAG SENPSISLHV IG LNGPTHD LEMMPPDDPR MREYYITMVK WATSTKVAVT WLNRAQNVSI LTLCDATTGV CTKKHEDESE AWLHRQNEEP VFS KDGRKF FFIRAIPQGG RGKFYHITVS SSQPNSSNDN IQSITSGDWD VTKILAYDEK GNKIYFLSTE DLPRRRQLYS ANTV GNFNR QCLSCDLVEN CTYFSASFSH SMDFFLLKCE GPGVPMVTVH NTTDKKKMFD LETNEHVKKA INDRQMPKVE YRDIE IDDY NLPMQILKPA TFTDTTHYPL LLVVDGTPGS QSVAEKFEVS WETVMVSSHG AVVVKCDGRG SGFQGTKLLH EVRRRL GLL EEKDQMEAVR TMLKEQYIDR TRVAVFGKDY GGYLSTYILP AKGENQGQTF TCGSALSPIT DFKLYASAFS ERYLGLH GL DNRAYEMTKV AHRVSALEEQ QFLIIHPTAD EKIHFQHTAE LITQLIRGKA NYSLQIYPDE SHYFTSSSLK QHLYRSII N FFVECFRI

UniProtKB: A-type potassium channel modulatory protein DPP6

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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: 4.0 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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