[English] 日本語
Yorodumi
- EMDB-8650: 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: 8650
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 3.7 Å resolution
AuthorsWang WW / MacKinnon R
CitationCell, 2017, 169, 422-430.e10

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

Validation ReportPDB-ID: 5va1

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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0075
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0075
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5va1
  • Surface level: 0.0075
  • 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_8650.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.
= 146.199 Å
256 pix
0.57 Å/pix.
= 146.299 Å
256 pix
0.48 Å/pix.
= 123.699 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: 0.57148 Å / Y: 0.57109 Å / Z: 0.4832 Å
Density
Contour Level:0.0075 (by author), 0.0075 (movie #1):
Minimum - Maximum-0.0077007296 - 0.025356712
Average (Standard dev.)0.0019453842 (0.0033561029)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA: 146.29887 Å / B: 146.19904 Å / C: 123.6992 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.571480468750.571089843750.48319921875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z146.299146.199123.699
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-0.0080.0250.002

-
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 141-380 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 141-380 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: 88.901664 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

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)

-
Image acquisition

Image acquisitionNumber of digital images: 4100
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 / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 213255
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
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)

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