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- EMDB-1675: Keap1 homodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-1675
TitleKeap1 homodimer
Map dataThis is an image of a surface rendered side-view of Keap1
Sample
  • Sample: Keap1
  • Protein or peptide: Keap1
KeywordsNrf2 / oxidative stress / single particle analysis / transmission electron microscopy / three-dimensional reconstruction
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / Resolution: 24.0 Å
AuthorsOgura T / Tong KI / Mio K / Maruyama Y / Kurokawa H / Sato C / Yamamoto M
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Keap1 is a forked-stem dimer structure with two large spheres enclosing the intervening, double glycine repeat, and C-terminal domains.
Authors: Toshihiko Ogura / Kit I Tong / Kazuhiro Mio / Yuusuke Maruyama / Hirofumi Kurokawa / Chikara Sato / Masayuki Yamamoto /
Abstract: Keap1 is a substrate adaptor of a Cullin 3-based E3 ubiquitin ligase complex that recognizes Nrf2, and also acts as a cellular sensor for xenobiotics and oxidative stresses. Nrf2 is a transcriptional ...Keap1 is a substrate adaptor of a Cullin 3-based E3 ubiquitin ligase complex that recognizes Nrf2, and also acts as a cellular sensor for xenobiotics and oxidative stresses. Nrf2 is a transcriptional factor regulating the expression of cytoprotective enzyme genes in response to such stresses. Under unstressed conditions Keap1 binds Nrf2 and results in rapid degradation of Nrf2 through the proteasome pathway. In contrast, upon exposure to oxidative and electrophilic stress, reactive cysteine residues in intervening region (IVR) and Broad complex, Tramtrack, and Bric-à-Brac domains of Keap1 are modified by electrophiles. This modification prevents Nrf2 from rapid degradation and induces Nrf2 activity by repression of Keap1. Here we report the structure of mouse Keap1 homodimer by single particle electron microscopy. Three-dimensional reconstruction at 24-A resolution revealed two large spheres attached by short linker arms to the sides of a small forked-stem structure, resembling a cherry-bob. Each sphere has a tunnel corresponding to the central hole of the beta-propeller domain, as determined by x-ray crystallography. The IVR domain appears to surround the core of the beta-propeller domain. The unexpected proximity of IVR to the beta-propeller domain suggests that any distortions generated during modification of reactive cysteine residues in the IVR domain may send a derepression signal to the beta-propeller domain and thereby stabilize Nrf2. This study thus provides a structural basis for the two-site binding and hinge-latch model of stress sensing by the Nrf2-Keap1 system.
History
DepositionJan 8, 2010-
Header (metadata) releaseApr 26, 2011-
Map releaseApr 26, 2011-
UpdateApr 26, 2011-
Current statusApr 26, 2011Processing site: PDBe / Status: Released

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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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1675.jpg

emd_1675.jpg

Downloads & links

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Map

FileDownload / File: emd_1675.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered side-view of Keap1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.92 Å/pix.
x 100 pix.
= 192. Å		1.92 Å/pix.
x 100 pix.
= 192. Å		1.92 Å/pix.
x 100 pix.
= 192. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 215.0 / Movie #1: 215
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)114.131 (±32.410400000000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 192 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: Keap1
  • Protein or peptide: Keap1

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Supramolecule #1000: Keap1

SupramoleculeName: Keap1 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: One homodimer of Keap1 / Number unique components: 1
Molecular weightExperimental: 155 KDa / Theoretical: 141 KDa

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Macromolecule #1: Keap1

MacromoleculeName: Keap1 / type: protein_or_peptide / ID: 1 / Name.synonym: Keap1 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse / Location in cell: Cytoplasm
Molecular weightExperimental: 155 KDa / Theoretical: 141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 100CX
Image recordingDigitization - Sampling interval: 10 µm / Number real images: 92 / Bits/pixel: 16
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Top entry / Specimen holder model: JEOL

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPINNS

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