[English] 日本語
Yorodumi
- EMDB-32334: CryoEM structure of human KChIP2-Kv4.3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32334
TitleCryoEM structure of human KChIP2-Kv4.3 complex
Map data
Sample
  • Complex: Complex of voltage-gated potassium channel Kv4.3 with KChIP2
    • Protein or peptide: Kv channel-interacting protein 2
    • Protein or peptide: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / ER retention sequence binding / positive regulation of voltage-gated potassium channel activity / Kv4.2-KChIP2 channel complex / clustering of voltage-gated potassium channels / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / positive regulation of potassium ion export across plasma membrane / potassium channel complex / membrane repolarization during ventricular cardiac muscle cell action potential ...ventricular cardiac muscle cell membrane repolarization / ER retention sequence binding / positive regulation of voltage-gated potassium channel activity / Kv4.2-KChIP2 channel complex / clustering of voltage-gated potassium channels / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / positive regulation of potassium ion export across plasma membrane / potassium channel complex / membrane repolarization during ventricular cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / membrane repolarization / Voltage gated Potassium channels / postsynaptic specialization membrane / regulation of potassium ion transmembrane transport / regulation of heart contraction / action potential / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / potassium channel activity / detection of calcium ion / GABA-ergic synapse / potassium channel regulator activity / voltage-gated potassium channel complex / muscle contraction / sarcolemma / protein homooligomerization / potassium ion transport / chemical synaptic transmission / postsynaptic membrane / transmembrane transporter binding / dendritic spine / neuronal cell body / dendrite / synapse / calcium ion binding / protein-containing complex binding / signal transduction / identical protein binding / 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 / EF-hand domain pair / 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
Similarity search - Domain/homology
Kv channel-interacting protein 2 / Potassium voltage-gated channel subfamily D member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMa DM / Guo JT
Funding support4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021FZZX001-28
Ministry of Science and Technology (MoST, China)LD21H020001
National Natural Science Foundation of China (NSFC)LR19C050002
National Natural Science Foundation of China (NSFC)LY19H020007
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, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32334.png

Downloads & links

-
Map

FileDownload / File: emd_32334.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.0109
Minimum - Maximum-0.05346814 - 0.09232946
Average (Standard dev.)-3.1259344e-05 (±0.0024764526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 273.78003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Complex of voltage-gated potassium channel Kv4.3 with KChIP2

EntireName: Complex of voltage-gated potassium channel Kv4.3 with KChIP2
Components
  • Complex: Complex of voltage-gated potassium channel Kv4.3 with KChIP2
    • Protein or peptide: Kv channel-interacting protein 2
    • Protein or peptide: Isoform 2 of Potassium voltage-gated channel subfamily D member 3

-
Supramolecule #1: Complex of voltage-gated potassium channel Kv4.3 with KChIP2

SupramoleculeName: Complex of voltage-gated potassium channel Kv4.3 with KChIP2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: Kv channel-interacting protein 2

MacromoleculeName: Kv channel-interacting protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.693582 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRGQGRKESL SDSRDLDGSY DQLTGHPPGP TKKALKQRFL KLLPCCGPQA LPSVSETLAA PASLRPHRPR LLDPDSVDDE FELSTVCHR PEGLEQLQEQ TKFTRKELQV LYRGFKNECP SGIVNEENFK QIYSQFFPQG DSSTYATFLF NAFDTNHDGS V SFEDFVAG ...String:
MRGQGRKESL SDSRDLDGSY DQLTGHPPGP TKKALKQRFL KLLPCCGPQA LPSVSETLAA PASLRPHRPR LLDPDSVDDE FELSTVCHR PEGLEQLQEQ TKFTRKELQV LYRGFKNECP SGIVNEENFK QIYSQFFPQG DSSTYATFLF NAFDTNHDGS V SFEDFVAG LSVILRGTVD DRLNWAFNLY DLNKDGCITK EEMLDIMKSI YDMMGKYTYP ALREEAPREH VESFFQKMDR NK DGVVTIE EFIESCQKDE NIMRSMQLFD NVILEGGSSG GHHHHHHHH

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

MacromoleculeName: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.472781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGVAAWLP FARAAAIGWM PVANCPMPLA PADKNKRQDE LIVLNVSGRR FQTWRTTLER YPDTLLGSTE KEFFFNEDTK EYFFDRDPE VFRCVLNFYR TGKLHYPRYE CISAYDDELA FYGILPEIIG DCCYEEYKDR KRENAERLMD DNDSENNQES M PSLSFRQT ...String:
MAAGVAAWLP FARAAAIGWM PVANCPMPLA PADKNKRQDE LIVLNVSGRR FQTWRTTLER YPDTLLGSTE KEFFFNEDTK EYFFDRDPE VFRCVLNFYR TGKLHYPRYE CISAYDDELA FYGILPEIIG DCCYEEYKDR KRENAERLMD DNDSENNQES M PSLSFRQT MWRAFENPHT STLALVFYYV TGFFIAVSVI TNVVETVPCG TVPGSKELPC GERYSVAFFC LDTACVMIFT VE YLLRLFA APSRYRFIRS VMSIIDVVAI MPYYIGLVMT NNEDVSGAFV TLRVFRVFRI FKFSRHSQGL RILGYTLKSC ASE LGFLLF SLTMAIIIFA TVMFYAEKGS SASKFTSIPA SFWYTIVTMT TLGYGDMVPK TIAGKIFGSI CSLSGVLVIA LPVP VIVSN FSRIYHQNQR ADKRRAQKKA RLARIRVAKT GSSNAYLHSK RNGLLNEALE LTGTPEEEHM GKTTSLIESQ HHHLL HCLE KTTNHEFIDE QMFEQNCMES SMQNYPSTRS PSLSSHPGLT TTCCSRRSKK TTHLPNSNLP ATRLRSMQEL STIHIQ GSE QPSLTTSRSS LNLKADDGLR PNCKTSQITT AIISIPTPPA LTPEGESRPP PASPGPNTNI PSIASNVVKV SAL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 240437

+
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