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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
Samplehuman ether-a-go-go related K+ channel hERG
SourceHomo sapiens / human
Map datahuman ether-a-go-go related K+ channel
Methodsingle particle reconstruction, at 4 Å resolution
AuthorsWang WW / MacKinnon R
CitationCell, 2017, 169, 422-430.e10

Cell, 2017, 169, 422-430.e10 StrPapers
Cryo-EM Structure of the Open Human Ether-à-go-go-Related K(+) Channel hERG.
Weiwei Wang / Roderick MacKinnon

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
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Supplemental images

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Map

Fileemd_8652.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

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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
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

Specimen stateparticle
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

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