[English] 日本語
Yorodumi
- EMDB-69841: Cryo-EM structure of the human KCNQ2/KCNQ3 heterotetramer (3:1 st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-69841
TitleCryo-EM structure of the human KCNQ2/KCNQ3 heterotetramer (3:1 stoichiometry) with CLM142 (M2223 CLM142, without symmetry expansion)
Map data
Sample
  • Complex: the human KCNQ2/KCNQ3 heterotetramer (3:1 stoichiometry)
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
    • Protein or peptide: Green fluorescent protein,Potassium voltage-gated channel subfamily KQT member 2
  • Ligand: ~{N}-(7-cyclopropyl-1-prop-2-ynyl-indazol-3-yl)-4-fluoranyl-benzamide
  • Ligand: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
  • Ligand: (2R)-2-{[(4-O-hexopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-4-{[(25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
Keywordspotassium channels / MEMBRANE PROTEIN
Function / homology
Function and homology information


axon initial segment / Voltage gated Potassium channels / node of Ranvier / ankyrin binding / Interaction between L1 and Ankyrins / voltage-gated monoatomic cation channel activity / action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport ...axon initial segment / Voltage gated Potassium channels / node of Ranvier / ankyrin binding / Interaction between L1 and Ankyrins / voltage-gated monoatomic cation channel activity / action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / bioluminescence / generation of precursor metabolites and energy / nervous system development / chemical synaptic transmission / calmodulin binding / synapse / cell surface / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, KCNQ3 / Potassium channel, voltage dependent, KCNQ2 / Unstructured region on Potassium channel subunit alpha KvLQT2 / Ankyrin-G binding site / Ankyrin-G binding motif of KCNQ2-3 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Green fluorescent protein, GFP / Green fluorescent protein-related ...Potassium channel, voltage dependent, KCNQ3 / Potassium channel, voltage dependent, KCNQ2 / Unstructured region on Potassium channel subunit alpha KvLQT2 / Ankyrin-G binding site / Ankyrin-G binding motif of KCNQ2-3 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily KQT member 3 / Potassium voltage-gated channel subfamily KQT member 2 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsWang YF / Yang H / Qu YN / Shen HZ
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Vita / Year: 2026
Title: Structural basis for heteromeric assembly and subthreshold activation of human M-channel
Authors: Wang Y / Yang H / Qu Y / Li J / Li X / Hou W / Wu K / Xie G / Wang X / Ye Y / Yang H / Shen H
History
DepositionMar 22, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_69841.png

Downloads & links

-
Map

FileDownload / File: emd_69841.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44
Minimum - Maximum-5.125118 - 7.6069746
Average (Standard dev.)0.010716861 (±0.13497402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_69841_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_69841_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : the human KCNQ2/KCNQ3 heterotetramer (3:1 stoichiometry)

EntireName: the human KCNQ2/KCNQ3 heterotetramer (3:1 stoichiometry)
Components
  • Complex: the human KCNQ2/KCNQ3 heterotetramer (3:1 stoichiometry)
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
    • Protein or peptide: Green fluorescent protein,Potassium voltage-gated channel subfamily KQT member 2
  • Ligand: ~{N}-(7-cyclopropyl-1-prop-2-ynyl-indazol-3-yl)-4-fluoranyl-benzamide
  • Ligand: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
  • Ligand: (2R)-2-{[(4-O-hexopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-4-{[(25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside

-
Supramolecule #1: the human KCNQ2/KCNQ3 heterotetramer (3:1 stoichiometry)

SupramoleculeName: the human KCNQ2/KCNQ3 heterotetramer (3:1 stoichiometry)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Potassium voltage-gated channel subfamily KQT member 3

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 3
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.032938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASDYKDHDI DYKDDDDKGT MLSRPVKRNN AKYRRIQTLI YDALERPRGW ALLYHALVFL IVLGCLILAV LTTFKEYETV SGDWLLLLE TFAIFIFGAE FALRIWAAGC CCRYKGWRGR LKFARKPLCM LDIFVLIASV PVVAVGNQGN VLATSLRSLR F LQILRMLR ...String:
MASDYKDHDI DYKDDDDKGT MLSRPVKRNN AKYRRIQTLI YDALERPRGW ALLYHALVFL IVLGCLILAV LTTFKEYETV SGDWLLLLE TFAIFIFGAE FALRIWAAGC CCRYKGWRGR LKFARKPLCM LDIFVLIASV PVVAVGNQGN VLATSLRSLR F LQILRMLR MDRRGGTWKL LGSAICAHSK ELITAWYIGF LTLILSSFLV YLVEKDVPEV DAQGEEMKEE FETYADALWW GL ITLATIG YGDKTPKTWE GRLIAATFSL IGVSFFALPA GILGSGLALK VQEQHRQKHF EKRRKPAAEL IQAAWRYYAT NPN RIDLVA TWRFYESVVS FPFFRKEQLE AASSQKLGLL DRVRLSNPRG SNTKGKLFTP LNVDAIEESP SKEPKPVGLN NKER FRTAF RMKAYAFWQS SEDAGTGDPM AEDRGYGNDF PIEDMIPTLK AAIRAVRILQ FRLYKKKFKE TLRPYDVKDV IEQYS AGHL DMLSRIKYLQ TRIDMIFTPG PPSTPKHKKS QKGSAFTFPS QQSPRNEPYV ARPSTSEIED QSMMGKFVKV ERQVQD MGK KLDFLVDMHM QHMERLQVQV TEYYPTKGTS SPAEAEKKED NRYSDLKTII CNYSETG

UniProtKB: Potassium voltage-gated channel subfamily KQT member 3

-
Macromolecule #2: Green fluorescent protein,Potassium voltage-gated channel subfami...

MacromoleculeName: Green fluorescent protein,Potassium voltage-gated channel subfamily KQT member 2
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.657266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAMHHHHHHH HGGSMVSKGE ELFTGVVPIL VELDGDVNGH KFSVSGEGEG DATYGKLTLK FICTTGKLPV PWPTLVTTLT YGVQCFSRY PDHMKQHDFF KSAMPEGYVQ ERTIFFKDDG NYTTRAEVKF EGDTLVNRIE LKGIDFKEDG NILGHKLEYN Y NSHNVYIM ...String:
MAMHHHHHHH HGGSMVSKGE ELFTGVVPIL VELDGDVNGH KFSVSGEGEG DATYGKLTLK FICTTGKLPV PWPTLVTTLT YGVQCFSRY PDHMKQHDFF KSAMPEGYVQ ERTIFFKDDG NYTTRAEVKF EGDTLVNRIE LKGIDFKEDG NILGHKLEYN Y NSHNVYIM ADKQKNGIKV NFKIRHNIED GSVQLADHYQ QNTPIGDGPV LLPDNHYLST QSKLSKDPNE KRDHMVLLEF VT AAGITLG MDELYKSGLR SGLEVLFQGP GGRMAGKPPK RNAFYRKLQN FLYNVLERPR GWAFIYHAYV FLLVFSCLVL SVF STIKEY EKSSEGALYI LEIVTIVVFG VEYFVRIWAA GCCCRYRGWR GRLKFARKPF CVIDIMVLIA SIAVLAAGSQ GNVF ATSAL RSLRFLQILR MIRMDRRGGT WKLLGSVVYA HSKELVTAWY IGFLCLILAS FLVYLAEKGE NDHFDTYADA LWWGL ITLT TIGYGDKYPQ TWNGRLLAAT FTLIGVSFFA LPAGILGSGF ALKVQEQHRQ KHFEKRRNPA AGLIQSAWRF YATNLS GGG SGGGSPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI EQYSAGHLDM LSRIKSLQSR VDQIVGRGPA ITDKDRT KG PAEAELPEDP SMMGRLGKVE KQVLSMEKKL DFLVNIYMQR MGIPPTETEA YFGAKEPEPA PPYHSPEDSR EHVDRHGC I VKIVRSSSST GQKNFSVEGG SSGGWSHPQF EK

UniProtKB: Green fluorescent protein, Potassium voltage-gated channel subfamily KQT member 2, Potassium voltage-gated channel subfamily KQT member 2

-
Macromolecule #3: ~{N}-(7-cyclopropyl-1-prop-2-ynyl-indazol-3-yl)-4-fluoranyl-benzamide

MacromoleculeName: ~{N}-(7-cyclopropyl-1-prop-2-ynyl-indazol-3-yl)-4-fluoranyl-benzamide
type: ligand / ID: 3 / Number of copies: 4 / Formula: A1E7E
Molecular weightTheoretical: 333.359 Da

-
Macromolecule #4: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoy...

MacromoleculeName: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
type: ligand / ID: 4 / Number of copies: 3 / Formula: 9PE
Molecular weightTheoretical: 593.773 Da
Chemical component information

ChemComp-9PE:
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate / phospholipid*YM

-
Macromolecule #5: (2R)-2-{[(4-O-hexopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-4-{...

MacromoleculeName: (2R)-2-{[(4-O-hexopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-4-{[(25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
type: ligand / ID: 5 / Number of copies: 3 / Formula: YJ0
Molecular weightTheoretical: 1.165315 KDa
Chemical component information

ChemComp-YJ0:
(2R)-2-{[(4-O-hexopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-4-{[(25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 15162
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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