Journal: Protein Sci / Year: 2016 Title: The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7. Authors: Jason W Schmidberger / Mehdi Sharifi Tabar / Mario Torrado / Ana P G Silva / Michael J Landsberg / Lou Brillault / Saad AlQarni / Yi Cheng Zeng / Benjamin L Parker / Jason K K Low / Joel P Mackay / Abstract: The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed ...The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed across multiple tissues in organisms ranging from mammals to nematode worms. In common with other chromatin-remodeling complexes, however, its molecular mechanism of action is not well understood and only limited structural information is available to show how the complex is assembled. As a step towards understanding the structure of the NuRD complex, we have characterized the interaction between two subunits: the metastasis associated protein MTA1 and the histone-binding protein RBBP4. We show that MTA1 can bind to two molecules of RBBP4 and present negative stain electron microscopy and chemical crosslinking data that allow us to build a low-resolution model of an MTA1-(RBBP4)2 subcomplex. These data build on our understanding of NuRD complex structure and move us closer towards an understanding of the biochemical basis for the activity of this complex.
History
Deposition
May 9, 2016
-
Header (metadata) release
May 18, 2016
-
Map release
May 18, 2016
-
Update
Aug 24, 2016
-
Current status
Aug 24, 2016
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_3431.map.gz / Format: CCP4 / Size: 538.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Human MTA1 truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
Voxel size
X=Y=Z: 5.58 Å
Density
Contour Level
By AUTHOR: 0.068 / Movie #1: 0.068
Minimum - Maximum
-0.31457576 - 0.4855015
Average (Standard dev.)
-0.01756996 (±0.05386001)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
52
52
52
Spacing
52
52
52
Cell
A=B=C: 290.16 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
5.58
5.58
5.58
M x/y/z
52
52
52
origin x/y/z
0.000
0.000
0.000
length x/y/z
290.160
290.160
290.160
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
52
52
52
D min/max/mean
-0.315
0.486
-0.018
-
Supplemental data
-
Sample components
-
Entire : Human MTA1 C-terminal truncation mutant (residues 449 to 715) bou...
Entire
Name: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
Components
Sample: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
Protein or peptide: Metastasis-associated protein MTA1 C-terminus (449-715)
Protein or peptide: Histone-binding protein RBBP4
-
Supramolecule #1000: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bou...
Supramolecule
Name: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4. type: sample / ID: 1000 Oligomeric state: One copy of MTA1-C binds to two copies of RBBP4. Number unique components: 2
pH: 8.2 / Details: 50 mM HEPES KOH pH 8.2, 150 mM NaCl, 1 mM DTT.
Staining
Type: NEGATIVE Details: After an incubation time of 5 min, the grid was blotted and washed with five drops of distilled water, blotted again and subsequently stained with a 2% (w/v) uranyl acetate solution for one ...Details: After an incubation time of 5 min, the grid was blotted and washed with five drops of distilled water, blotted again and subsequently stained with a 2% (w/v) uranyl acetate solution for one minute. Excess stain was then blotted away and the grid allowed to dry under air at ambient conditions.
Particles were initially selected manually (1730 particles) then these were used to autopick 12114 particles using RELION. This was reduced to 9000 particles using manual inspection. Use of 2D class averaging reduced count to 4000 particles which were used to generate four 3D classes.
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 4000
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi