Biotechnology and Biological Sciences Research Council (BBSRC)
BB/N002954/1
United Kingdom
Medical Research Council (MRC, United Kingdom)
MC_PC_171136
United Kingdom
Citation
Journal: Nucleic Acids Res / Year: 2015 Title: Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting. Authors: Toshimasa Itoh / Louise Fairall / Frederick W Muskett / Charles P Milano / Peter J Watson / Nadia Arnaudo / Almutasem Saleh / Christopher J Millard / Mohammed El-Mezgueldi / Fabrizio Martino ...Authors: Toshimasa Itoh / Louise Fairall / Frederick W Muskett / Charles P Milano / Peter J Watson / Nadia Arnaudo / Almutasem Saleh / Christopher J Millard / Mohammed El-Mezgueldi / Fabrizio Martino / John W R Schwabe / Abstract: Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and ...Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and contains histone deacetylases 1 and 2, the MIDEAS corepressor protein and a protein called DNTTIP1 whose function was hitherto poorly understood. Here, we report the structures of two domains from DNTTIP1. The amino-terminal region forms a tight dimerization domain with a novel structural fold that interacts with and mediates assembly of the HDAC1:MIDEAS complex. The carboxy-terminal domain of DNTTIP1 has a structure related to the SKI/SNO/DAC domain, despite lacking obvious sequence homology. We show that this domain in DNTTIP1 mediates interaction with both DNA and nucleosomes. Thus, DNTTIP1 acts as a dimeric chromatin binding module in the HDAC1:MIDEAS corepressor complex.
History
Deposition
May 16, 2020
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Header (metadata) release
Jul 8, 2020
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Map release
Jul 8, 2020
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Update
May 22, 2024
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Current status
May 22, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Entire : Dimeric complex of the MiDAC deacetylase complex containing HDAC1...
Entire
Name: Dimeric complex of the MiDAC deacetylase complex containing HDAC1, the ELM2-SANT domain of MIDEAS and the dimerisation domain of DNTTIP1
Components
Complex: Dimeric complex of the MiDAC deacetylase complex containing HDAC1, the ELM2-SANT domain of MIDEAS and the dimerisation domain of DNTTIP1
Protein or peptide: Histone deacetylase 1
Protein or peptide: Deoxynucleotidyltransferase terminal-interacting protein 1
Protein or peptide: Mitotic deacetylase-associated SANT domain protein
Ligand: INOSITOL HEXAKISPHOSPHATE
Ligand: ZINC ION
Ligand: POTASSIUM ION
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Supramolecule #1: Dimeric complex of the MiDAC deacetylase complex containing HDAC1...
Supramolecule
Name: Dimeric complex of the MiDAC deacetylase complex containing HDAC1, the ELM2-SANT domain of MIDEAS and the dimerisation domain of DNTTIP1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weight
Theoretical: 65.409 Da
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Macromolecule #6: POTASSIUM ION
Macromolecule
Name: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: K
Molecular weight
Theoretical: 39.098 Da
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
0.45 mg/mL
Buffer
pH: 7.5 Component:
Concentration
Name
12.5 mM
HEPES
25.0 mM
potassium acetate
0.25 mM
TCEP
0.1 %
glutaraldehdye
50.0 mM
Tris/HCl
Grid
Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 30 sec at 30 mA
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 3 sec, blot force 10..
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Electron microscopy
Microscope
FEI TITAN KRIOS
Temperature
Min: 100.0 K / Max: 100.0 K
Specialist optics
Phase plate: VOLTA PHASE PLATE
Image recording
Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 2752 / Average exposure time: 60.0 sec. / Average electron dose: 36.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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