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

by single particle reconstruction, at 4 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.5, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.5, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5va3, Surface level: 1.5, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 8652
TitleCryo-EM structure of the human ether-a-go-go related K+ channel
Maphuman ether-a-go-go related K+ channel
Samplehuman ether-a-go-go related K+ channel hERG
AuthorsWang WW, MacKinnon R
DateDeposition: 2017-03-24, Header release: 2017-05-03, Map release: 2017-05-03, Last update: 2017-09-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.5, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.5, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5va3, Surface level: 1.5, Imaged by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-5va3

CiteFit

Cite: data citing same article

Fit: output model of fitting

Article
Citation - Primary
ArticleCell, Vol. 169, Issue 3, Page 422-430.e10, Year 2017
TitleCryo-EM Structure of the Open Human Ether-à-go-go-Related K(+) Channel hERG.
AuthorsWeiwei Wang, Roderick MacKinnon
Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.
KeywordsAmino Acid Sequence, Cryoelectron Microscopy, ERG1 Potassium Channel (chemistry), Humans, KCNH2 protein, human, Models, Molecular, Protein Conformation, Sequence Alignment
LinksPubMed: 28431243, PII: S0092-8674(17)30410-5, DOI: 10.1016/j.cell.2017.03.048, PMC: PMC5484391
Map
Fileemd_8652.map.gz ( map file in CCP4 format, 67109 KB )
Projections & SlicesSize of images:
AxesY (Sec.)X (Row.)Z (Col.)
256 pix
0.56562890625 A/pix
= 144.801 A
256 pix
0.56562890625 A/pix
= 144.801 A
256 pix
0.46444921875 A/pix
= 118.899 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Density
Contour Level:1.5 (by author), 1.5 (movie #1):
Minimum - Maximum: -2.0461385 - 6.3207603
Average (Standard dev.): 0.4593979 (0.7881963)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderZXY
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
Unit CellA: 144.80128 A, B: 144.80128 A, C: 118.8992 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX: 0.56563 A, Y: 0.56563 A, Z: 0.46445 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-2.0466.3210.459
Annotation Detailshuman ether-a-go-go related K+ channel
Supplement
Images
Images
Sample
Namehuman ether-a-go-go related K+ channel hERG
Number of Components2
DetailsTruncated hERG construct hERGTs (amino acid residues 141-380 and 871-1005 deleted) with S631A mutation
Component #1: cellular-component - human ether-a-go-go related K+ channel hERG
Scientific namehuman ether-a-go-go related K+ channel hERG
DetailsTruncated hERG construct hERGTs (amino acid residues 141-380 and 871-1005 deleted) with S631A mutation
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Exp System Cell: HEK293S GnTI-
Vector: BacMam
Component #2: protein - Potassium voltage-gated channel subfamily H member 2
Scientific namePotassium voltage-gated channel subfamily H member 2
Theoretical Mass0.088885664 MDa
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Vector: BacMam
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc6 mg/ml
BufferpH: 7.4
Details: pH 7.4, adjusted with NaOH
Vitrification
Cryogen NameETHANE
Humidity98
Temperature298 Kelvin
InstrumentFEI VITROBOT MARK IV
Detailsone blot: 3 second blot time, 0 blot force
Imaging
MicroscopeFEI TITAN KRIOS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose85 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationCalibrated: 38461
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 3500 nm
Specimen Holder
ModelFEI TITAN KRIOS AUTOGRID HOLDER
Camera
DetectorGATAN K2 (4k x 4k)
Image Acquisition
#1
Number of Digital Images1505
Details50 0.3-second frames were collected for each movie at a dose rate of ~1.8 e-/A2/frame
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmFOURIER SPACE
SoftwareFREALIGN
Resolution By Author4 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC4 (4 fold cyclic)
Number of Projections206
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-8652-v19.xml (7.2 KB)
emd-8652-v20.xml (15.9 KB)
emd-8652.xml (7.2 KB)
Map dataemd_8652.map.gz (57 MB)
Imagesemd_8652.png (186.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-8652
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 6.3 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 6.3 MB
Session file for UCSF-Chimera, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 7.1 MB
Session file for UCSF-Chimera, 1.7 MB