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- PDB-6v01: structure of human KCNQ1-KCNE3-CaM complex with PIP2 -

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Basic information

Entry
Database: PDB / ID: 6v01
Titlestructure of human KCNQ1-KCNE3-CaM complex with PIP2
Components
  • Calmodulin-1
  • Potassium voltage-gated channel subfamily E member 3,Potassium voltage-gated channel subfamily E member 3
  • Potassium voltage-gated channel subfamily KQT member 1
KeywordsMEMBRANE PROTEIN / potassium channel / KCNQ1 / CaM
Function / homology
Function and homology information


negative regulation of membrane repolarization during ventricular cardiac muscle cell action potential / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / negative regulation of voltage-gated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of gastric acid secretion / negative regulation of potassium ion export across plasma membrane / regulation of atrial cardiac muscle cell membrane repolarization / 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 / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / negative regulation of voltage-gated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of gastric acid secretion / negative regulation of potassium ion export across plasma membrane / regulation of atrial cardiac muscle cell membrane repolarization / 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 / potassium ion export across plasma membrane / atrial cardiac muscle cell action potential / positive regulation of voltage-gated calcium channel activity / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization / positive regulation of cardiac muscle contraction / negative regulation of delayed rectifier potassium channel activity / ion channel complex / outward rectifier potassium channel activity / regulation of ventricular cardiac muscle cell membrane repolarization / positive regulation of potassium ion transmembrane transport / delayed rectifier potassium channel activity / gene silencing / ventricular cardiac muscle cell action potential / positive regulation of heart rate / cardiac conduction / protein phosphatase 1 binding / cardiovascular system development / glycogen catabolic process / neuronal cell body membrane / intestinal absorption / regulation of heart rate by cardiac conduction / regulation of gene expression by genetic imprinting / inositol phosphate metabolic process / potassium channel regulator activity / regulation of rhodopsin mediated signaling pathway / N-terminal myristoylation domain binding / Wnt signaling pathway, calcium modulating pathway / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / regulation of cell communication by electrical coupling involved in cardiac conduction / potassium ion transmembrane transport / adenylate cyclase activator activity / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / catalytic complex / detection of calcium ion / renal absorption / adenylate cyclase binding / voltage-gated potassium channel activity / protein kinase A regulatory subunit binding / voltage-gated potassium channel complex / inner ear development / positive regulation of protein dephosphorylation / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / regulation of heart contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cardiac muscle contraction / positive regulation of phosphoprotein phosphatase activity / cofactor metabolic process / protein kinase A catalytic subunit binding / protein serine/threonine kinase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / calcium channel complex / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / muscle contraction / substantia nigra development / cellular response to epinephrine stimulus / sarcomere / regulation of heart rate / positive regulation of protein serine/threonine kinase activity / positive regulation of protein autophosphorylation / regulation of nitric-oxide synthase activity / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of peptidyl-threonine phosphorylation / cellular response to cAMP / regulation of cytokinesis / sensory perception of sound / calcium-mediated signaling / spindle microtubule / cytoplasmic vesicle membrane / response to calcium ion / cellular response to drug / spindle pole / platelet degranulation / Fc-epsilon receptor signaling pathway / scaffold protein binding / late endosome / disordered domain specific binding / ion channel binding / vesicle / basolateral plasma membrane / perikaryon / calmodulin binding / lysosome / early endosome
Slow voltage-gated potassium channel / Voltage-gated potassium channel / Potassium channel, voltage-dependent, beta subunit, KCNE / EF-hand domain / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage-dependent, beta subunit, KCNE3 / Ion transport domain / Potassium channel, voltage dependent, KCNQ1 / EF-hand domain pair / EF-Hand 1, calcium-binding site ...Slow voltage-gated potassium channel / Voltage-gated potassium channel / Potassium channel, voltage-dependent, beta subunit, KCNE / EF-hand domain / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage-dependent, beta subunit, KCNE3 / Ion transport domain / Potassium channel, voltage dependent, KCNQ1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / Potassium channel, voltage dependent, KCNQ, C-terminal / Calmodulin / EF-hand domain pair / Ion transport protein / KCNQ voltage-gated potassium channel
Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 1 / Potassium voltage-gated channel subfamily E member 3
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMackinnon, R. / Sun, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute5K99HL143037 United States
Howard Hughes Medical Institute United States
CitationJournal: To Be Published
Title: Structural basis of human KCNQ1 modulation and gating
Authors: Mackinnon, R. / Sun, J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release

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Assembly

Deposited unit
B: Calmodulin-1
C: Potassium voltage-gated channel subfamily E member 3,Potassium voltage-gated channel subfamily E member 3
E: Calmodulin-1
F: Potassium voltage-gated channel subfamily E member 3,Potassium voltage-gated channel subfamily E member 3
H: Calmodulin-1
I: Potassium voltage-gated channel subfamily E member 3,Potassium voltage-gated channel subfamily E member 3
K: Calmodulin-1
L: Potassium voltage-gated channel subfamily E member 3,Potassium voltage-gated channel subfamily E member 3
A: Potassium voltage-gated channel subfamily KQT member 1
J: Potassium voltage-gated channel subfamily KQT member 1
D: Potassium voltage-gated channel subfamily KQT member 1
G: Potassium voltage-gated channel subfamily KQT member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,33424
Polymers480,82512
Non-polymers4,50912
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area46960 Å2
ΔGint-510 kcal/mol
Surface area102250 Å2

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Components

#1: Protein/peptide
Calmodulin-1 /


Mass: 16852.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Homo sapiens (human) / References: UniProt: P0DP23
#2: Protein/peptide
Potassium voltage-gated channel subfamily E member 3,Potassium voltage-gated channel subfamily E member 3 / MinK-related peptide 2 / Minimum potassium ion channel-related peptide 2 / Potassium channel subunit beta MiRP2


Mass: 40095.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNE3 / Production host: Homo sapiens (human) / References: UniProt: Q9Y6H6
#3: Protein/peptide
Potassium voltage-gated channel subfamily KQT member 1 / IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1 / KQT-like 1 / Voltage-gated potassium channel subunit Kv7.1


Mass: 63258.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ1, KCNA8, KCNA9, KVLQT1 / Production host: Homo sapiens (human) / References: UniProt: P51787
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Calcium
#5: Chemical
ChemComp-PT5 / (1S)-2-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (8E,11E)-icosa-5,8,11,14-tetraenoate / Phosphatidylinositol 4,5-bisphosphate / PtdIns(4,5)P2


Mass: 1047.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H85O19P3 / Phosphatidylinositol 4,5-bisphosphate / Comment: phospholipid *YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KCNQ1-CaM complex / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 94 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73640 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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