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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 data
SampleKCNQ1-CaM complex
  • Potassium voltage-gated channel subfamily KQT member 1
  • Calmodulin-1
  • MCherry fluorescent protein,Potassium voltage-gated channel subfamily E member 3
  • ligand
Function / homology
Function and homology information


negative regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of voltage-gated potassium channel activity / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / regulation of gastric acid secretion / negative regulation of potassium ion export across plasma membrane / regulation of atrial cardiac muscle cell membrane repolarization / membrane repolarization during atrial cardiac muscle cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during ventricular cardiac muscle cell action potential ...negative regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of voltage-gated potassium channel activity / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / regulation of gastric acid secretion / negative regulation of potassium ion export across plasma membrane / regulation of atrial cardiac muscle cell membrane repolarization / membrane repolarization during atrial cardiac muscle cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during action potential / positive regulation of voltage-gated calcium channel activity / membrane repolarization during cardiac muscle cell action potential / atrial cardiac muscle cell action potential / potassium ion export across plasma membrane / regulation of membrane repolarization / ion channel complex / outward rectifier potassium channel activity / negative regulation of delayed rectifier potassium channel activity / regulation of ventricular cardiac muscle cell membrane repolarization / positive regulation of potassium ion transmembrane transport / gene silencing / positive regulation of cardiac muscle contraction / delayed rectifier potassium channel activity / ventricular cardiac muscle cell action potential / cardiac conduction / positive regulation of heart rate / protein phosphatase 1 binding / circulatory system development => GO:0072359 / neuronal cell body membrane / regulation of heart rate by cardiac conduction / regulation of gene expression by genetic imprinting / potassium channel regulator activity / intestinal absorption / glycogen catabolic process / establishment of protein localization to mitochondrial membrane / N-terminal myristoylation domain binding / type 3 metabotropic glutamate receptor binding / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / regulation of high voltage-gated calcium channel activity / protein phosphatase activator activity / regulation of synaptic vesicle endocytosis / positive regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / regulation of rhodopsin mediated signaling pathway / renal absorption / positive regulation of cyclic-nucleotide phosphodiesterase activity / detection of calcium ion / catalytic complex / adenylate cyclase binding / protein kinase A regulatory subunit binding / response to corticosterone / inositol phosphate metabolic process / adenylate cyclase activator activity / inner ear development / voltage-gated potassium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of heart contraction / calcium channel inhibitor activity / activation of adenylate cyclase activity / Wnt signaling pathway, calcium modulating pathway / positive regulation of phosphoprotein phosphatase activity / nitric-oxide synthase binding / protein kinase A catalytic subunit binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / voltage-gated potassium channel complex / titin binding / substantia nigra development / calcium channel complex / sarcomere / cellular response to epinephrine stimulus / positive regulation of protein dephosphorylation / regulation of heart rate / phosphatidylinositol 3-kinase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein serine/threonine kinase activator activity / enzyme regulator activity / positive regulation of protein autophosphorylation / mitochondrial membrane / bioluminescence / response to amphetamine / generation of precursor metabolites and energy / positive regulation of peptidyl-threonine phosphorylation / cellular response to cAMP / positive regulation of protein serine/threonine kinase activity / regulation of cytokinesis / regulation of nitric-oxide synthase activity / nitric-oxide synthase regulator activity / phosphatidylinositol-4,5-bisphosphate binding / regulation of synaptic vesicle exocytosis / positive regulation of DNA binding / sensory perception of sound / spindle microtubule / synaptic vesicle membrane / calcium-mediated signaling / muscle contraction
Potassium channel, voltage-dependent, beta subunit, KCNE / EF-Hand 1, calcium-binding site / Green fluorescent protein, GFP / EF-hand domain / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage-dependent, beta subunit, KCNE3 / Ion transport domain / Potassium channel, voltage dependent, KCNQ1 / Green fluorescent protein-related / EF-hand domain pair ...Potassium channel, voltage-dependent, beta subunit, KCNE / EF-Hand 1, calcium-binding site / Green fluorescent protein, GFP / EF-hand domain / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage-dependent, beta subunit, KCNE3 / Ion transport domain / Potassium channel, voltage dependent, KCNQ1 / Green fluorescent protein-related / EF-hand domain pair / Potassium channel, voltage dependent, KCNQ, C-terminal / Green fluorescent protein / Voltage-gated potassium channel / Calmodulin
Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 1 / Potassium voltage-gated channel subfamily E member 3 / MCherry fluorescent protein
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.
Validation ReportPDB-ID: 6v00

SummaryFull reportAbout validation report
History
DepositionNov 16, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseDec 4, 2019-
UpdateFeb 5, 2020-
Current statusFeb 5, 2020Processing 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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Structure viewerEM map:
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Supplemental images

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)
Projections & slices

Image control

Size
Brightness
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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
Contour LevelBy AUTHOR: 6 / Movie #1: 6
Minimum - Maximum-19.06765 - 34.47205
Average (Standard dev.)0.00000000000 (±1)
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 / Number of components: 5

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Component #1: protein, KCNQ1-CaM complex

ProteinName: KCNQ1-CaM complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Potassium voltage-gated channel subfamily KQT member 1

ProteinName: Potassium voltage-gated channel subfamily KQT member 1
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 63.258574 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Calmodulin-1

ProteinName: Calmodulin-1 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 16.852545 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, MCherry fluorescent protein,Potassium voltage-gated chan...

ProteinName: MCherry fluorescent protein,Potassium voltage-gated channel subfamily E member 3
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 40.095168 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 94 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 39074
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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