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PDBj>EM Navigator>Detail page - EMDB-1675

Keap1 homodimer

by single particle reconstruction, at 24 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 215, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 215, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1675
TitleKeap1 homodimer
MapThis is an image of a surface rendered side-view of Keap1
SampleKeap1
KeywordsNrf2, oxidative stress, single particle analysis, transmission electron microscopy, three-dimensional reconstruction
AuthorsOgura T, Tong KI, Mio K, Maruyama Y, Kurokawa H, Sato C, Yamamoto M
DateDeposition: 2010-01-08, Header release: 2011-04-26, Map release: 2011-04-26, Last update: 2011-04-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 215, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 215, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 7, Page 2842-7, Year 2010
TitleKeap1 is a forked-stem dimer structure with two large spheres enclosing the intervening, double glycine repeat, and C-terminal domains.
AuthorsToshihiko Ogura, Kit I Tong, Kazuhiro Mio, Yuusuke Maruyama, Hirofumi Kurokawa, Chikara Sato, Masayuki Yamamoto
Neuroscience Research Institute and Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 1-1-4 Umezono, Tsukuba 305-8568, Japan.
KeywordsAdaptor Proteins, Signal Transducing (chemistry), Animals, Crystallography, X-Ray, Cytoskeletal Proteins (chemistry), Dimerization, Keap1 protein, mouse, Mice, Microscopy, Electron, Transmission, Models, Molecular, NF-E2-Related Factor 2 (metabolism), Protein Binding, Protein Conformation, Protein Structure, Tertiary (genetics)
LinksDOI: 10.1073/pnas.0914036107, PubMed: 20133743, PMC: PMC2840362
Map
Fileemd_1675.map.gz ( map file in CCP4 format, 3908 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
1.92 A/pix
= 192. A
100 pix
1.92 A/pix
= 192. A
100 pix
1.92 A/pix
= 192. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:215 (by emdb), 215 (movie #1):
Minimum - Maximum: 0 - 255
Average (Standard dev.): 114.131 (32.4104)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
Unit CellA= B= C: 192 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.92 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.921.921.92
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z192.000192.000192.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean0.000255.000114.131
Annotation DetailsThis is an image of a surface rendered side-view of Keap1
Supplement
Images
Images
Sample
NameKeap1
Number of Components1
Oligomeric StateOne homodimer of Keap1
Theoretical Mass0.141MDa
DetailsThe sample was monodisperse
Experimental Mass0.155MDa
Component #1: protein - Keap1
Scientific nameKeap1
Theoretical Mass0.141 MDa
Experimental Mass0.155 MDa
Oligomeric DetailsDimer
Number of Copies2
Scientific Name of SpeciesMus musculus

Common Name of SpeciesMouse
NCBI taxonomy10090
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 100CX
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage100 kV
Illumination ModeOTHER
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderTop entry
ModelJEOL
Camera
Image Acquisition
#1
Number of Digital Images92
Sampling Size10
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmEcho-correlation method
SoftwareSPINNS
CTF CorrectionEach particle
Resolution By Author24 A
Resolution MethodFSC 0.5
Single Particle
Applied SymmetryC2 (2 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-1675.xml (6.3 KB)
Map dataemd_1675.map.gz (986.4 KB)
ImagesEMD-1675.jpg (39.6 KB)
emd_1675.jpg (39.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1675
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.4 KB