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- EMDB-20966: structure of human KCNQ1-KCNE3-CaM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20966
Titlestructure of human KCNQ1-KCNE3-CaM complex
Map datahuman KCNQ1-KCNE3-CaM
Sample
  • Complex: KCNQ1-CaM complex
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 1
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: MCherry fluorescent protein,Potassium voltage-gated channel subfamily E member 3
  • Ligand: CALCIUM ION
Keywordspotassium channel / KCNQ1 / CaM / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of membrane repolarization during ventricular cardiac muscle cell action potential / gastrin-induced gastric acid secretion / stomach development / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / negative regulation of voltage-gated potassium channel activity / basolateral part of cell / lumenal side of membrane / negative regulation of delayed rectifier potassium channel activity / rhythmic behavior ...negative regulation of membrane repolarization during ventricular cardiac muscle cell action potential / gastrin-induced gastric acid secretion / stomach development / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / negative regulation of voltage-gated potassium channel activity / basolateral part of cell / lumenal side of membrane / negative regulation of delayed rectifier potassium channel activity / rhythmic behavior / regulation of gastric acid secretion / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / Phase 3 - rapid repolarisation / membrane repolarization during action potential / negative regulation of potassium ion export across plasma membrane / auditory receptor cell development / membrane repolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / iodide transport / intracellular chloride ion homeostasis / regulation of atrial cardiac muscle cell membrane repolarization / membrane repolarization during ventricular cardiac muscle cell action potential / atrial cardiac muscle cell action potential / renal sodium ion absorption / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of membrane repolarization / detection of mechanical stimulus involved in sensory perception of sound / protein phosphatase 1 binding / potassium ion homeostasis / delayed rectifier potassium channel activity / ventricular cardiac muscle cell action potential / non-motile cilium assembly / regulation of ventricular cardiac muscle cell membrane repolarization / intestinal absorption / positive regulation of potassium ion transmembrane transport / Voltage gated Potassium channels / inner ear morphogenesis / outward rectifier potassium channel activity / regulation of heart contraction / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / cardiac muscle cell contraction / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / sodium ion transport / adrenergic receptor signaling pathway / PKA activation / CaMK IV-mediated phosphorylation of CREB / inner ear development / Glycogen breakdown (glycogenolysis) / monoatomic ion channel complex / renal absorption / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / autophagosome membrane docking / protein kinase A regulatory subunit binding / negative regulation of high voltage-gated calcium channel activity / ciliary base / protein kinase A catalytic subunit binding / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / neuronal cell body membrane / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / potassium ion import across plasma membrane / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / social behavior / regulation of heart rate by cardiac conduction / regulation of cell communication by electrical coupling involved in cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / cochlea development / protein phosphatase activator activity / action potential / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / potassium channel regulator activity / Smooth Muscle Contraction / voltage-gated potassium channel activity / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / cellular response to interferon-beta
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNE3 / Potassium channel, voltage-dependent, beta subunit, KCNE / Slow voltage-gated potassium channel / Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / : / Green fluorescent protein, GFP ...Potassium channel, voltage-dependent, beta subunit, KCNE3 / Potassium channel, voltage-dependent, beta subunit, KCNE / Slow voltage-gated potassium channel / Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / : / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 1 / Potassium voltage-gated channel subfamily E member 3 / MCherry fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMackinnon R / Sun J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5K99HL143037 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2020
Title: Structural Basis of Human KCNQ1 Modulation and Gating.
Authors: Ji Sun / Roderick MacKinnon /
Abstract: KCNQ1, also known as Kv7.1, is a voltage-dependent K channel that regulates gastric acid secretion, salt and glucose homeostasis, and heart rhythm. Its functional properties are regulated in a tissue- ...KCNQ1, also known as Kv7.1, is a voltage-dependent K channel that regulates gastric acid secretion, salt and glucose homeostasis, and heart rhythm. Its functional properties are regulated in a tissue-specific manner through co-assembly with beta subunits KCNE1-5. In non-excitable cells, KCNQ1 forms a complex with KCNE3, which suppresses channel closure at negative membrane voltages that otherwise would close it. Pore opening is regulated by the signaling lipid PIP2. Using cryoelectron microscopy (cryo-EM), we show that KCNE3 tucks its single-membrane-spanning helix against KCNQ1, at a location that appears to lock the voltage sensor in its depolarized conformation. Without PIP2, the pore remains closed. Upon addition, PIP2 occupies a site on KCNQ1 within the inner membrane leaflet, which triggers a large conformational change that leads to dilation of the pore's gate. It is likely that this mechanism of PIP2 activation is conserved among Kv7 channels.
History
DepositionNov 16, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseDec 4, 2019-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v00
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20966.png

Downloads & links

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Map

FileDownload / File: emd_20966.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman KCNQ1-KCNE3-CaM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.03 Å/pix.
x 300 pix.
= 309. Å		1.03 Å/pix.
x 300 pix.
= 309. Å		1.03 Å/pix.
x 300 pix.
= 309. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-19.06765 - 34.472050000000003
Average (Standard dev.)0.000000000001565 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 309.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z309.000309.000309.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-19.06834.4720.000

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Supplemental data

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Sample components

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Entire : KCNQ1-CaM complex

EntireName: KCNQ1-CaM complex
Components
  • Complex: KCNQ1-CaM complex
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 1
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: MCherry fluorescent protein,Potassium voltage-gated channel subfamily E member 3
  • Ligand: CALCIUM ION

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Supramolecule #1: KCNQ1-CaM complex

SupramoleculeName: KCNQ1-CaM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.258574 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASDLGPRPP VSLDPRVSIY STRRPVLART HVQGRVYNFL ERPTGWKCFV YHFAVFLIVL VCLIFSVLST IEQYAALATG TLFWMEIVL VVFFGTEYVV RLWSAGCRSK YVGLWGRLRF ARKPISIIDL IVVVASMVVL CVGSKGQVFA TSAIRGIRFL Q ILRMLHVD ...String:
MASDLGPRPP VSLDPRVSIY STRRPVLART HVQGRVYNFL ERPTGWKCFV YHFAVFLIVL VCLIFSVLST IEQYAALATG TLFWMEIVL VVFFGTEYVV RLWSAGCRSK YVGLWGRLRF ARKPISIIDL IVVVASMVVL CVGSKGQVFA TSAIRGIRFL Q ILRMLHVD RQGGTWRLLG SVVFIHRQEL ITTLYIGFLG LIFSSYFVYL AEKDAVNESG RVEFGSYADA LWWGVVTVTT IG YGDKVPQ TWVGKTIASC FSVFAISFFA LPAGILGSGF ALKVQQKQRQ KHFNRQIPAA ASLIQTAWRC YAAENPDSST WKI YIRKAP RSHTLLSPSP KPKKSVVVKK KKFKLDKDNG VTPGEKMLTV PHITCDPPEE RRLDHFSVDG YDSSVRKSPT LLEV SMPHF MRTNSFAEDL DLEGETLLTP ITHISQLREH HRATIKVIRR MQYFVAKKKF QQARKPYDVR DVIEQYSQGH LNLMV RIKE LQRRLDQSIG KPSLFISVSE KSKDRGSNTI GARLNRVEDK VTQLDQRLAL ITDMLHQLLS LHSNSLEVLF QGP

UniProtKB: Potassium voltage-gated channel subfamily KQT member 1

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #3: MCherry fluorescent protein,Potassium voltage-gated channel subfa...

MacromoleculeName: MCherry fluorescent protein,Potassium voltage-gated channel subfamily E member 3
type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.095168 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGMVSKGEED NMAIIKEFMR FKVHMEGSVN GHEFEIEGEG EGRPYEGTQT AKLKVTKGGP LPFAWDILSP QFMYGSKAYV KHPADIPDY LKLSFPEGFN WERVMNFEDG GVVTVTQDSS LQDGEFIYKV KLRGTNFPSD GPVMQCRTMG WEASTERMYP E DGALKGEI ...String:
GGMVSKGEED NMAIIKEFMR FKVHMEGSVN GHEFEIEGEG EGRPYEGTQT AKLKVTKGGP LPFAWDILSP QFMYGSKAYV KHPADIPDY LKLSFPEGFN WERVMNFEDG GVVTVTQDSS LQDGEFIYKV KLRGTNFPSD GPVMQCRTMG WEASTERMYP E DGALKGEI KQRLKLKDGG HYDAEVKTTY KAKKPVQLPG AYNVDIKLDI LSHNEDYTIV EQYERAEGRH STGGMDELYK GS GENLYFQ SSRATMETTN GTETWYESLH AVLKALNATL HSNLLCRPGP GLGPDNQTEE RRASLPGRDD NSYMYILFVM FLF AVTVGS LILGYTRSRK VDKRSDPYHV YIKNRVSMI

UniProtKB: MCherry fluorescent protein, Potassium voltage-gated channel subfamily E member 3

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 94.0 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

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 39074
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6v00:
structure of human KCNQ1-KCNE3-CaM complex

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