[English] 日本語
Yorodumi
- EMDB-31019: CryoEM structure of human Kv4.2-DPP6S-KChIP1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31019
TitleCryoEM structure of human Kv4.2-DPP6S-KChIP1 complex
Map datamap H
Sample
  • Complex: human Kv4.2-DPP6S-KChIP1 complex
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6
    • Protein or peptide: Kv channel-interacting protein 1
    • Protein or peptide: Potassium voltage-gated channel subfamily D member 2
    • Protein or peptide: Kv channel-interacting protein 1
Keywordsmembrane protein
Function / homology
Function and homology information


Kv4.3-KChIP1 channel complex / 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 / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / anchoring junction ...Kv4.3-KChIP1 channel complex / 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 / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / anchoring junction / postsynaptic specialization membrane / regulation of heart contraction / neuronal cell body membrane / plasma membrane raft / locomotor rhythm / action potential / voltage-gated potassium channel activity / potassium channel activity / neuronal action potential / potassium channel regulator activity / voltage-gated potassium channel complex / GABA-ergic synapse / muscle contraction / sensory perception of pain / potassium ion transmembrane transport / serine-type peptidase activity / protein localization to plasma membrane / protein homooligomerization / cytoplasmic side of plasma membrane / cellular response to hypoxia / chemical synaptic transmission / perikaryon / postsynaptic membrane / transmembrane transporter binding / dendritic spine / neuronal cell body / glutamatergic synapse / calcium ion binding / dendrite / synapse / proteolysis / membrane / metal ion binding / plasma membrane / cytoplasm
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 / Recoverin family / 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 / Recoverin family / 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 / EF-hand domain pair / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
A-type potassium channel modulatory protein DPP6 / A-type potassium channel modulatory protein KCNIP1 / A-type voltage-gated potassium channel KCND2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0072
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0072
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7e8h
  • Surface level: 0.0072
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7e8h
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31019.png

Downloads & links

-
Map

FileDownload / File: emd_31019.map.gz / Format: CCP4 / Size: 101 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap H
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 298 pix.
= 298.799 Å		1 Å/pix.
x 298 pix.
= 298.799 Å		1 Å/pix.
x 298 pix.
= 298.799 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.00268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0072 / Movie #1: 0.0072
Minimum - Maximum-0.015678514 - 0.041326907
Average (Standard dev.)0.00045475256 (±0.0020708293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions298298298
Spacing298298298
CellA=B=C: 298.7986 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.00268120805371.00268120805371.0026812080537
M x/y/z298298298
origin x/y/z0.0000.0000.000
length x/y/z298.799298.799298.799
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS298298298
D min/max/mean-0.0160.0410.000

-
Supplemental data

-
Mask #1

Fileemd_31019_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_31019_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_31019_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human Kv4.2-DPP6S-KChIP1 complex

EntireName: human Kv4.2-DPP6S-KChIP1 complex
Components
  • Complex: human Kv4.2-DPP6S-KChIP1 complex
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6
    • Protein or peptide: Kv channel-interacting protein 1
    • Protein or peptide: Potassium voltage-gated channel subfamily D member 2
    • Protein or peptide: Kv channel-interacting protein 1

-
Supramolecule #1: human Kv4.2-DPP6S-KChIP1 complex

SupramoleculeName: human Kv4.2-DPP6S-KChIP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Dipeptidyl aminopeptidase-like protein 6

MacromoleculeName: Dipeptidyl aminopeptidase-like protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.277664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AKGIAIALLV ILVICSLIVT SVILLTPAED NSLSQKKKVT VEDLFSEDFK IHDPEAKWIS DTEFIYREQK GTVRLWNVET NTSTVLIEG KKIESLRAIR YEISPDREYA LFSYNVEPIY QHSYTGYYVL SKIPHGDPQS LDPPEVSNAK LQYAGWGPKG Q QLIFIFEN ...String:
AKGIAIALLV 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

-
Macromolecule #2: Dipeptidyl aminopeptidase-like protein 6

MacromoleculeName: Dipeptidyl aminopeptidase-like protein 6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.490898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAAAKGIAIA LLVILVICSL IVTSVILLTP AEDNSLSQKK KVTVEDLFSE DFKIHDPEAK WISDTEFIYR EQKGTVRLWN VETNTSTVL IEGKKIESLR AIRYEISPDR EYALFSYNVE PIYQHSYTGY YVLSKIPHGD PQSLDPPEVS NAKLQYAGWG P KGQQLIFI ...String:
AAAAKGIAIA LLVILVICSL IVTSVILLTP AEDNSLSQKK KVTVEDLFSE DFKIHDPEAK WISDTEFIYR EQKGTVRLWN VETNTSTVL IEGKKIESLR AIRYEISPDR EYALFSYNVE PIYQHSYTGY YVLSKIPHGD PQSLDPPEVS NAKLQYAGWG P KGQQLIFI FENNIYYCAH VGKQAIRVVS TGKEGVIYNG LSDWLYEEEI LKTHIAHWWS PDGTRLAYAA INDSRVPIME LP TYTGSIY PTVKPYHYPK AGSENPSISL HVIGLNGPTH DLEMMPPDDP RMREYYITMV KWATSTKVAV TWLNRAQNVS ILT LCDATT GVCTKKHEDE SEAWLHRQNE EPVFSKDGRK FFFIRAIPQG GRGKFYHITV SSSQPNSSND NIQSITSGDW DVTK ILAYD EKGNKIYFLS TEDLPRRRQL YSANTVGNFN RQCLSCDLVE NCTYFSASFS HSMDFFLLKC EGPGVPMVTV HNTTD KKKM FDLETNEHVK KAINDRQMPK VEYRDIEIDD YNLPMQILKP ATFTDTTHYP LLLVVDGTPG SQSVAEKFEV SWETVM VSS HGAVVVKCDG RGSGFQGTKL LHEVRRRLGL LEEKDQMEAV RTMLKEQYID RTRVAVFGKD YGGYLSTYIL PAKGENQ GQ TFTCGSALSP ITDFKLYASA FSERYLGLHG LDNRAYEMTK VAHRVSALEE QQFLIIHPTA DEKIHFQHTA ELITQLIR G KANYSLQIYP DESHYFTSSS LKQHLYRSII NFFVECFRI

UniProtKB: A-type potassium channel modulatory protein DPP6

-
Macromolecule #3: Kv channel-interacting protein 1

MacromoleculeName: Kv channel-interacting protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.145826 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EGLEQLEAQT NFTKRELQVL YRGFKNECPS GVVNEDTFKQ IYAQFFPHGD ASTYAHYLFN AFDTTQTGSV KFEDFVTALS ILLRGTVHE KLRWTFNLYD INKDGYINKE EMMDIVKAIY DMMGKYTYPV LKEDTPRQHV DVFFQKMDKN KDGIVTLDEF L ESCQEDDN IMRSLQLFQN VM

UniProtKB: A-type potassium channel modulatory protein KCNIP1

-
Macromolecule #4: Potassium voltage-gated channel subfamily D member 2

MacromoleculeName: Potassium voltage-gated channel subfamily D member 2 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.755738 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAGVAAWLPF ARAAAIGWMP VASGPMPAPP RQERKRTQDA LIVLNVSGTR FQTWQDTLER YPDTLLGSSE RDFFYHPETQ QYFFDRDPD IFRHILNFYR TGKLHYPRHE CISAYDEELA FFGLIPEIIG DCCYEEYKDR RRENAERLQD DADTDTAGES A LPTMTARQ ...String:
AAGVAAWLPF ARAAAIGWMP VASGPMPAPP RQERKRTQDA LIVLNVSGTR FQTWQDTLER YPDTLLGSSE RDFFYHPETQ QYFFDRDPD IFRHILNFYR TGKLHYPRHE CISAYDEELA FFGLIPEIIG DCCYEEYKDR RRENAERLQD DADTDTAGES A LPTMTARQ RVWRAFENPH TSTMALVFYY VTGFFIAVSV IANVVETVPC GSSPGHIKEL PCGERYAVAF FCLDTACVMI FT VEYLLRL AAAPSRYRFV RSVMSIIDVV AILPYYIGLV MTDNEDVSGA FVTLRVFRVF RIFKFSRHSQ GLRILGYTLK SCA SELGFL LFSLTMAIII FATVMFYAEK GSSASKFTSI PAAFWYTIVT MTTLGYGDMV PKTIAGKIFG SICSLSGVLV IALP VPVIV SNFSRIYHQN QRADKRRAQK KARLARIRAA KSGSANAYMQ SKRSGLLSNQ LQSSEDEQAF VSKSGSSFET QHHHL LHCL EKTTNHEFVD

UniProtKB: A-type voltage-gated potassium channel KCND2

-
Macromolecule #5: Kv channel-interacting protein 1

MacromoleculeName: Kv channel-interacting protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.242941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PEGLEQLEAQ TNFTKRELQV LYRGFKNECP SGVVNEDTFK QIYAQFFPHG DASTYAHYLF NAFDTTQTGS VKFEDFVTAL SILLRGTVH EKLRWTFNLY DINKDGYINK EEMMDIVKAI YDMMGKYTYP VLKEDTPRQH VDVFFQKMDK NKDGIVTLDE F LESCQEDD NIMRSLQLFQ NVM

UniProtKB: A-type potassium channel modulatory protein KCNIP1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139524
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more