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- EMDB-8651: Cryo-EM structure of the human ether-a-go-go related K+ channel -

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Basic information

Entry
Database: EMDB / ID: 8651
TitleCryo-EM structure of the human ether-a-go-go related K+ channel
Map datahERG truncation construct hERGT
Samplehuman ether-a-go-go related K+ channel hERG
  • Potassium voltage-gated channel subfamily H member 2
Function / homologyCyclic nucleotide-binding domain / PAS repeat profile. / PAS domain / Ion transport protein / Potassium channel, voltage-dependent, ERG / Ion transport domain / PAS-associated, C-terminal / PAS domain / cAMP/cGMP binding motif profile. / RmlC-like jelly roll fold ...Cyclic nucleotide-binding domain / PAS repeat profile. / PAS domain / Ion transport protein / Potassium channel, voltage-dependent, ERG / Ion transport domain / PAS-associated, C-terminal / PAS domain / cAMP/cGMP binding motif profile. / RmlC-like jelly roll fold / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding-like / PAC domain profile. / Voltage gated Potassium channels / Voltage-dependent channel domain superfamily / Phase 3 - rapid repolarisation / Cyclic nucleotide-binding domain / PAS domain superfamily / PAC motif / negative regulation of potassium ion export / inward rectifier potassium channel complex / regulation of heart rate by hormone / potassium ion homeostasis / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / potassium ion export across plasma membrane / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during ventricular cardiac muscle cell action potential / potassium ion export / membrane repolarization during action potential / membrane repolarization during cardiac muscle cell action potential / membrane repolarization / regulation of membrane repolarization / negative regulation of potassium ion transmembrane transport / delayed rectifier potassium channel activity / regulation of ventricular cardiac muscle cell membrane repolarization / inward rectifier potassium channel activity / positive regulation of potassium ion transmembrane transport / membrane depolarization during action potential / ventricular cardiac muscle cell action potential / regulation of heart rate by cardiac conduction / C3HC4-type RING finger domain binding / regulation of potassium ion transmembrane transport / potassium ion transmembrane transport / regulation of membrane potential / voltage-gated potassium channel complex / voltage-gated potassium channel activity / cardiac muscle contraction / phosphorelay sensor kinase activity / cellular response to drug / scaffold protein binding / ubiquitin protein ligase binding / cell surface / perinuclear region of cytoplasm / protein homodimerization activity / identical protein binding / plasma membrane / Potassium voltage-gated channel subfamily H member 2
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsWang WW / MacKinnon R
CitationJournal: Cell / Year: 2017
Title: Cryo-EM Structure of the Open Human Ether-à-go-go-Related K Channel hERG.
Authors: Weiwei Wang / Roderick MacKinnon
Abstract: The human ether-à-go-go-related potassium channel (hERG, Kv11.1) is a voltage-dependent channel known for its role in repolarizing the cardiac action potential. hERG alteration by mutation or ...The human ether-à-go-go-related potassium channel (hERG, Kv11.1) is a voltage-dependent channel known for its role in repolarizing the cardiac action potential. hERG alteration by mutation or pharmacological inhibition produces Long QT syndrome and the lethal cardiac arrhythmia torsade de pointes. We have determined the molecular structure of hERG to 3.8 Å using cryo-electron microscopy. In this structure, the voltage sensors adopt a depolarized conformation, and the pore is open. The central cavity has an atypically small central volume surrounded by four deep hydrophobic pockets, which may explain hERG's unusual sensitivity to many drugs. A subtle structural feature of the hERG selectivity filter might correlate with its fast inactivation rate, which is key to hERG's role in cardiac action potential repolarization.
Validation ReportPDB-ID: 5va2

SummaryFull reportAbout validation report
DateDeposition: Mar 24, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5va2
  • Surface level: 1.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8651.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
256 pix
0.57 Å/pix.
= 146.701 Å
256 pix
0.57 Å/pix.
= 146.701 Å
256 pix
0.47 Å/pix.
= 120.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.57305 Å / Y: 0.57305 Å / Z: 0.46914 Å
Density
Contour Level:1.8 (by author), 1.8 (movie #1):
Minimum - Maximum-1.8676711 - 6.150801
Average (Standard dev.)0.4355108 (0.8527215)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA: 146.7008 Å / B: 146.7008 Å / C: 120.09984 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.573050781250.573050781250.469140625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z146.701146.701120.100
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.8686.1510.436

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Supplemental data

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Sample components

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Entire human ether-a-go-go related K+ channel hERG

EntireName: human ether-a-go-go related K+ channel hERG
Details: Truncated hERG construct hERGTs (amino acid residues 141-350 and 871-1005 deleted)
Number of components: 2

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Component #1: cellular-component, human ether-a-go-go related K+ channel hERG

Cellular-componentName: human ether-a-go-go related K+ channel hERG
Details: Truncated hERG construct hERGTs (amino acid residues 141-350 and 871-1005 deleted)
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: BacMam / Cell of expression system: HEK293S GnTI-

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

ProteinName: Potassium voltage-gated channel subfamily H member 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 92.280539 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 6 mg/ml / Buffer solution: pH 7.4, adjusted with NaOH / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 98 % / Details: one blot: 3 second blot time, 0 blot force.

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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: 85 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 38461. X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2443
Details: 50 0.3-second frames were collected for each movie at a dose rate of ~1.8 e-/A2/frame

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 144
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: Fourier Shell Correlation / Refinement space: RECIPROCAL / Overall bvalue: 15
Output model

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