[English] 日本語
Yorodumi
- PDB-7w6t: CryoEM structure of human KChIP1-Kv4.3-DPP6 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w6t
TitleCryoEM structure of human KChIP1-Kv4.3-DPP6 complex
Components
  • Dipeptidyl aminopeptidase-like protein 6
  • Isoform 2 of Potassium voltage-gated channel subfamily D member 3
  • Kv channel-interacting protein 1
KeywordsMEMBRANE PROTEIN / Kv channel-interacting protein 1 Potassium voltage-gated channel Dipeptidyl aminopeptidase-like protein 6
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane ...ventricular cardiac muscle cell membrane repolarization / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane / voltage-gated potassium channel activity / potassium channel activity / regulation of heart rate by cardiac conduction / GABA-ergic synapse / potassium channel regulator activity / voltage-gated potassium channel complex / serine-type peptidase activity / potassium ion transport / protein homooligomerization / cytoplasmic side of plasma membrane / sarcolemma / postsynaptic membrane / transmembrane transporter binding / dendritic spine / neuronal cell body / calcium ion binding / dendrite / proteolysis / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv4, C-terminal / Shal-type voltage-gated potassium channels, N-terminal / Domain of unknown function (DUF3399) / Recoverin family / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain ...Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv4, C-terminal / Shal-type voltage-gated potassium channels, N-terminal / Domain of unknown function (DUF3399) / 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
Dipeptidyl aminopeptidase-like protein 6 / Kv channel-interacting protein 1 / Potassium voltage-gated channel subfamily D member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsMa, D.M. / Guo, J.T.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021FZZX001-28 China
Ministry of Science and Technology (MoST, China)LD21H020001 China
National Natural Science Foundation of China (NSFC)LR19C050002 China
National Natural Science Foundation of China (NSFC)LY19H020007 China
CitationJournal: Cell Res / Year: 2022
Title: Structural basis for the gating modulation of Kv4.3 by auxiliary subunits.
Authors: Demin Ma / Cheng Zhao / Xiaochen Wang / Xiaoxiao Li / Yi Zha / Yan Zhang / Guosheng Fu / Ping Liang / Jiangtao Guo / Dongwu Lai /
History
DepositionDec 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kv channel-interacting protein 1
B: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
E: Kv channel-interacting protein 1
F: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
G: Kv channel-interacting protein 1
H: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
I: Dipeptidyl aminopeptidase-like protein 6
J: Dipeptidyl aminopeptidase-like protein 6


Theoretical massNumber of molelcules
Total (without water)591,38110
Polymers591,38110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Kv channel-interacting protein 1 / KChIP1 / A-type potassium channel modulatory protein 1 / Potassium channel-interacting protein 1 / ...KChIP1 / A-type potassium channel modulatory protein 1 / Potassium channel-interacting protein 1 / Vesicle APC-binding protein


Mass: 26935.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNIP1, KCHIP1, VABP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NZI2
#2: Protein
Isoform 2 of Potassium voltage-gated channel subfamily D member 3 / Voltage-gated potassium channel subunit Kv4.3


Mass: 71472.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCND3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9UK17
#3: Protein Dipeptidyl aminopeptidase-like protein 6


Mass: 98874.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dpp6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: E9PWX1

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex of voltage-gated potassium channel Kv4.3 with auxiliary subunits KChIP1 and DPP6
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Mus musculus (house mouse)10090
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -1300 nm / Nominal defocus min: -1100 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 2.8 sec. / Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 263176 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00632618
ELECTRON MICROSCOPYf_angle_d0.75644168
ELECTRON MICROSCOPYf_dihedral_angle_d7.35819402
ELECTRON MICROSCOPYf_chiral_restr0.0464868
ELECTRON MICROSCOPYf_plane_restr0.0055622

+
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://pdbjlvh1.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