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- EMDB-8652: Cryo-EM structure of the human ether-a-go-go related K+ channel -

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Basic information

Entry
Database: EMDB / ID: 8652
TitleCryo-EM structure of the human ether-a-go-go related K+ channel
Map datahuman ether-a-go-go related K+ channel
Samplehuman ether-a-go-go related K+ channel hERG
  • Potassium voltage-gated channel subfamily H member 2
Function/homologynegative regulation of potassium ion export / inward rectifier potassium channel complex / Potassium channel, voltage-dependent, ERG / regulation of heart rate by hormone / potassium ion homeostasis / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / Phase 3 - rapid repolarisation / 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 ...negative regulation of potassium ion export / inward rectifier potassium channel complex / Potassium channel, voltage-dependent, ERG / regulation of heart rate by hormone / potassium ion homeostasis / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / Phase 3 - rapid repolarisation / 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 / membrane repolarization during action potential / potassium ion export / membrane repolarization during cardiac muscle cell action potential / membrane repolarization / negative regulation of potassium ion transmembrane transport / Voltage gated Potassium channels / delayed rectifier potassium channel activity / regulation of membrane repolarization / regulation of ventricular cardiac muscle cell membrane repolarization / membrane depolarization during action potential / inward rectifier potassium channel activity / positive regulation of potassium ion transmembrane transport / cardiac conduction / ventricular cardiac muscle cell action potential / Potassium channel, voltage-dependent, EAG/ELK/ERG / regulation of heart rate by cardiac conduction / C3HC4-type RING finger domain binding / regulation of potassium ion transmembrane transport / PAS-associated, C-terminal / PAC domain profile. / PAC motif / potassium ion transmembrane transport / Voltage-dependent channel domain superfamily / PAS domain / voltage-gated potassium channel activity / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding-like / voltage-gated potassium channel complex / cardiac muscle contraction / regulation of membrane potential / phosphorelay sensor kinase activity / Ion transport domain / Cyclic nucleotide-binding domain / Ion transport protein / RmlC-like jelly roll fold / PAS repeat profile. / PAS domain / PAS domain superfamily / cellular response to drug / scaffold protein binding / ubiquitin protein ligase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / identical protein binding / plasma membrane / Potassium voltage-gated channel subfamily H member 2
Function and homology information
SourceHomo sapiens / / human
MethodCryo EM / single particle reconstruction / 4 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.
Copyright: 2017 Elsevier Inc. All rights reserved.
Validation ReportPDB-ID: 5va3

SummaryFull reportAbout validation report
DateDeposition: Mar 24, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5va3
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

emd_8652.png

Downloads & links

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Map

Fileemd_8652.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.
= 144.801 Å		256 pix
0.57 Å/pix.
= 144.801 Å		256 pix
0.46 Å/pix.
= 118.899 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.56563 Å / Y: 0.56563 Å / Z: 0.46445 Å
Density

Histogram

Histogram (log scale)
Contour Level:1.5 (by author), 1.5 (movie #1):
Minimum - Maximum-2.0461385 - 6.3207603
Average (Standard dev.)0.4593979 (0.7881963)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA: 144.80128 Å / B: 144.80128 Å / C: 118.8992 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.565628906250.565628906250.46444921875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z144.801144.801118.899
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-2.0466.3210.459

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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 141-380 and 871-1005 deleted) with S631A mutation
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 141-380 and 871-1005 deleted) with S631A mutation
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 / Recombinant expression: No
MassTheoretical: 88.885664 kDa
Source (engineered)Expression System: Homo sapiens / / human / Vector: BacMam

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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 - 3500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1505
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 / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 206
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

5va3

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