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- EMDB-69845: Cryo-EM structure of the human wild-type KCNQ2/KCNQ3 heterotetram... -

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Basic information

Entry
Database: EMDB / ID: EMD-69845
TitleCryo-EM structure of the human wild-type KCNQ2/KCNQ3 heterotetramer (2:2 stoichiometry) in apo state (M2323 WT, 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: (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: 3.58 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

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Structure visualization

Supplemental images

emd_69845.png

Downloads & links

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Map

FileDownload / File: emd_69845.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: 0.494
Minimum - Maximum-2.4574962 - 3.9645967
Average (Standard dev.)0.009667927 (±0.08575143)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_69845_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69845_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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: (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

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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)

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.19982 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASDYKDHDI DYKDDDDKGT MGLKARRAAG AAGGGGDGGG GGGGAANPAG GDAAAAGDEE RKVGLAPGDV EQVTLALGAG ADKDGTLLL EGGGRDEGQR RTPQGIGLLA KTPLSRPVKR NNAKYRRIQT LIYDALERPR GWALLYHALV FLIVLGCLIL A VLTTFKEY ...String:
MASDYKDHDI DYKDDDDKGT MGLKARRAAG AAGGGGDGGG GGGGAANPAG GDAAAAGDEE RKVGLAPGDV EQVTLALGAG ADKDGTLLL EGGGRDEGQR RTPQGIGLLA KTPLSRPVKR NNAKYRRIQT LIYDALERPR GWALLYHALV FLIVLGCLIL A VLTTFKEY ETVSGDWLLL LETFAIFIFG AEFALRIWAA GCCCRYKGWR GRLKFARKPL CMLDIFVLIA SVPVVAVGNQ GN VLATSLR SLRFLQILRM LRMDRRGGTW KLLGSAICAH SKELITAWYI GFLTLILSSF LVYLVEKDVP EVDAQGEEMK EEF ETYADA LWWGLITLAT IGYGDKTPKT WEGRLIAATF SLIGVSFFAL PAGILGSGLA LKVQEQHRQK HFEKRRKPAA ELIQ AAWRY YATNPNRIDL VATWRFYESV VSFPFFRKEQ LEAASSQKLG LLDRVRLSNP RGSNTKGKLF TPLNVDAIEE SPSKE PKPV GLNNKERFRT AFRMKAYAFW QSSEDAGTGD PMAEDRGYGN DFPIEDMIPT LKAAIRAVRI LQFRLYKKKF KETLRP YDV KDVIEQYSAG HLDMLSRIKY LQTRIDMIFT PGPPSTPKHK KSQKGSAFTF PSQQSPRNEP YVARPSTSEI EDQSMMG KF VKVERQVQDM GKKLDFLVDM HMQHMERLQV QVTEYYPTKG TSSPAEAEKK EDNRYSDLKT IICNYSETGP PEPPYSFH Q VTIDKVSPYG FFAHDPVNLP RGGPSSGKVQ ATPPSSATTY VERPTVLPIL TLLDSRVSCH SQADLQGPYS DRISPRQRR SITRDSDTPL SLMSVNHEEL ERSPSGFSIS QDRDDYVFGP NGGSSWMREK RYLAEGETDT DTDPFTPSGS MPLSSTGDGI SDSVWTPSN KPI

UniProtKB: Potassium voltage-gated channel subfamily KQT member 3

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 126.318734 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 GGRMVQKSRN GGVYPGPSGE KKLKVGFVGL DPGAPDSTRD GALLIAGSEA PKR GSILSK PRAGGAGAGK PPKRNAFYRK LQNFLYNVLE RPRGWAFIYH AYVFLLVFSC LVLSVFSTIK EYEKSSEGAL YILE IVTIV VFGVEYFVRI WAAGCCCRYR GWRGRLKFAR KPFCVIDIMV LIASIAVLAA GSQGNVFATS ALRSLRFLQI LRMIR MDRR GGTWKLLGSV VYAHSKELVT AWYIGFLCLI LASFLVYLAE KGENDHFDTY ADALWWGLIT LTTIGYGDKY PQTWNG RLL AATFTLIGVS FFALPAGILG SGFALKVQEQ HRQKHFEKRR NPAAGLIQSA WRFYATNLSR TDLHSTWQYY ERTVTVP MY SSQTQTYGAS RLIPPLNQLE LLRNLKSKSG LAFRKDPPPE PSPSKGSPCR GPLCGCCPGR SSQKVSLKDR VFSSPRGV A AKGKGSPQAQ TVRRSPSADQ SLEDSPSKVP KSWSFGDRSR ARQAFRIKGA ASRQNSEEAS LPGEDIVDDK SCPCEFVTE DLTPGLKVSI RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS RIKSLQSRVD QIVGRGPAIT DKDRTKGPAE AELPEDPSM MGRLGKVEKQ VLSMEKKLDF LVNIYMQRMG IPPTETEAYF GAKEPEPAPP YHSPEDSREH VDRHGCIVKI V RSSSSTGQ KNFSAPPAAP PVQCPPSTSW QPQSHPRQGH GTSPVGDHGS LVRIPPPPAH ERSLSAYGGG NRASMEFLRQ ED TPGCRPP EGNLRDSDTS ISIPSVDHEE LERSFSGFSI SQSKENLDAL NSCYAAVAPC AKVRPYIAEG ESDTDSDLCT PCG PPPRSA TGEGPFGDVG WAGPRK

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

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Macromolecule #3: (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: 3 / Number of copies: 2 / 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

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Macromolecule #4: (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: 4 / Number of copies: 2 / 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

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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

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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 50903
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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