[English] 日本語
Yorodumi
- EMDB-8651: Cryo-EM structure of the human ether-a-go-go related K+ channel -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8651
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 datahERG truncation construct hERGT
Methodsingle particle reconstruction, at 3.8 A 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

DateDeposition: Mar 24, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Mar 24, 2017

-
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
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5va2
  • Surface level: 1.8
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
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 A/pix
= 146.701 A
256 pix
0.57 A/pix
= 146.701 A
256 pix
0.47 A/pix
= 120.1 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.57305 A / Y: 0.57305 A / Z: 0.46914 A
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
Origin000
Limit255255255
Spacing256256256
CellA: 146.7008 A / B: 146.7008 A / C: 120.09984 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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

-
Supplemental data

-
Sample components

-
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

-
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-

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

ProteinName: Potassium voltage-gated channel subfamily H member 2 / Recombinant expression: No
MassTheoretical: 92.280539 kDa
Source (engineered)Expression System: Homo sapiens / human / Vector: BacMam

+
Experimental details

-
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

-
Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 85 e/A2 / 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)

-
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

-
Image processing

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

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more