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- EMDB-1675: Keap1 homodimer -

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Basic information

Entry
Database: EMDB / ID: 1675
TitleKeap1 homodimer
KeywordsNrf2 / oxidative stress / single particle analysis / transmission electron microscopy / three-dimensional reconstruction
SampleKeap1
SourceMus musculus / mammal / Mouse / ハツカネズミ, はつかねずみ /
Map dataThis is an image of a surface rendered side-view of Keap1
Methodsingle particle reconstruction, at 24 A resolution
AuthorsOgura T / Tong KI / Mio K / Maruyama Y / Kurokawa H / Sato C / Yamamoto M
CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 2842-2847

Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 2842-2847 StrPapers
Keap1 is a forked-stem dimer structure with two large spheres enclosing the intervening, double glycine repeat, and C-terminal domains.
Toshihiko Ogura / Kit I Tong / Kazuhiro Mio / Yuusuke Maruyama / Hirofumi Kurokawa / Chikara Sato / Masayuki Yamamoto

DateDeposition: Jan 8, 2010 / Header (metadata) release: Apr 26, 2011 / Map release: Apr 26, 2011 / Last update: Jan 8, 2010

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 215
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 215
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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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.

Voxel sizeX=Y=Z: 1.92 A
Density
Contour Level:215 (by emdb), 215 (movie #1):
Minimum - Maximum0 - 255
Average (Standard dev.)114.131 (32.4104)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
CellA=B=C: 192 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean0.000255.000114.131

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Supplemental data

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Sample components

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Entire Keap1

EntireName: Keap1 / Details: The sample was monodisperse / Number of components: 1 / Oligomeric State: One homodimer of Keap1
MassTheoretical: 141 kDa / Experimental: 155 kDa

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Component #1: protein, Keap1

ProteinName: Keap1 / a.k.a: Keap1 / Oligomeric Details: Dimer / Recombinant expression: Yes / Number of Copies: 2
MassTheoretical: 141 kDa / Experimental: 155 kDa
SourceSpecies: Mus musculus / mammal / Mouse / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 100CX
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Top entry / Model: JEOL

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Image acquisition

Image acquisitionNumber of digital images: 92 / Sampling size: 10 microns / Bit depth: 16

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic)
3D reconstructionAlgorithm: Echo-correlation method / Software: SPINNS / CTF correction: Each particle / Resolution: 24 A / Resolution method: FSC 0.5

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