[English] 日本語
Yorodumi
- EMDB-11042: The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11042
TitleThe structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex
Map data
Sample
  • Complex: Tetrameric 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: ZINC ION
  • Ligand: POTASSIUM ION
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsHDAC1 MIDEAS ELMSAN1 DNTTIP1 TDIF1 histone deacetylase MiDAC / GENE REGULATION
Function / homology
Function and homology information


Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / negative regulation of androgen receptor signaling pathway / fungiform papilla formation / NuRD complex ...Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / negative regulation of androgen receptor signaling pathway / fungiform papilla formation / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / endoderm development / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / protein deacetylation / Regulation of MITF-M-dependent genes involved in apoptosis / STAT3 nuclear events downstream of ALK signaling / Transcription of E2F targets under negative control by DREAM complex / histone deacetylase / DNA methylation-dependent constitutive heterochromatin formation / protein lysine deacetylase activity / positive regulation of signaling receptor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / histone deacetylase activity / positive regulation of oligodendrocyte differentiation / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / Notch-HLH transcription pathway / eyelid development in camera-type eye / Sin3-type complex / E-box binding / cellular response to platelet-derived growth factor stimulus / oligodendrocyte differentiation / odontogenesis of dentin-containing tooth / RNA Polymerase I Transcription Initiation / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / G0 and Early G1 / NF-kappaB binding / negative regulation by host of viral transcription / nucleosome binding / RNA polymerase II core promoter sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of intrinsic apoptotic signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / heterochromatin / core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of canonical NF-kappaB signal transduction / MECP2 regulates neuronal receptors and channels / Regulation of TP53 Activity through Acetylation / transcription repressor complex / SUMOylation of chromatin organization proteins / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of PTEN gene transcription / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / promoter-specific chromatin binding / hippocampus development / Deactivation of the beta-catenin transactivating complex / positive regulation of smooth muscle cell proliferation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / heterochromatin formation / neuron differentiation / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription corepressor activity / p53 binding / chromatin organization / chromosome / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / neuronal cell body / positive regulation of cell population proliferation
Similarity search - Function
Terminal deoxynucleotidyltransferase-interacting factor 1 / DNTTIP1, dimerisation domain / : / DNTTIP1 dimerisation domain / TdIF1, C-terminal / : / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 ...Terminal deoxynucleotidyltransferase-interacting factor 1 / DNTTIP1, dimerisation domain / : / DNTTIP1 dimerisation domain / TdIF1, C-terminal / : / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone deacetylase / SANT domain profile. / SANT domain / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Ureohydrolase domain superfamily / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Histone deacetylase 1 / Mitotic deacetylase-associated SANT domain protein / Deoxynucleotidyltransferase terminal-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsFairall L / Saleh A
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust100237/Z/12/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N002954/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_171136 United Kingdom
CitationJournal: 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
DepositionMay 16, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6z2k
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11042.png

Downloads & links

-
Map

FileDownload / File: emd_11042.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.018
Minimum - Maximum-0.036822643 - 0.060755543
Average (Standard dev.)0.00007943722 (±0.0012748084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0370.0610.000

-
Supplemental data

-
Mask #1

Fileemd_11042_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11042_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_11042_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tetrameric complex of the MiDAC deacetylase complex containing HD...

EntireName: Tetrameric complex of the MiDAC deacetylase complex containing HDAC1, the ELM2-SANT domain of MIDEAS and the dimerisation domain of DNTTIP1
Components
  • Complex: Tetrameric 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: ZINC ION
  • Ligand: POTASSIUM ION
  • Ligand: INOSITOL HEXAKISPHOSPHATE

-
Supramolecule #1: Tetrameric complex of the MiDAC deacetylase complex containing HD...

SupramoleculeName: Tetrameric 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 357 KDa

-
Macromolecule #1: Histone deacetylase 1

MacromoleculeName: Histone deacetylase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.178906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSK QMQRFNVGED CPVFDGLFEF CQLSTGGSVA SAVKLNKQQT DIAVNWAGGL HHAKKSEASG FCYVNDIVLA I LELLKYHQ ...String:
MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSK QMQRFNVGED CPVFDGLFEF CQLSTGGSVA SAVKLNKQQT DIAVNWAGGL HHAKKSEASG FCYVNDIVLA I LELLKYHQ RVLYIDIDIH HGDGVEEAFY TTDRVMTVSF HKYGEYFPGT GDLRDIGAGK GKYYAVNYPL RDGIDDESYE AI FKPVMSK VMEMFQPSAV VLQCGSDSLS GDRLGCFNLT IKGHAKCVEF VKSFNLPMLM LGGGGYTIRN VARCWTYETA VAL DTEIPN ELPYNDYFEY FGPDFKLHIS PSNMTNQNTN EYLEKIKQRL FENLRMLPHA PGVQMQAIPE DAIPEESGDE DEDD PDKRI SICSSDKRIA CEEEFSDSEE EGEGGRKNSS NFKKAKRVKT EDEKEKDPEE KKEVTEEEKT KEEKPEAKGV KEEVK LA

UniProtKB: Histone deacetylase 1

-
Macromolecule #2: Deoxynucleotidyltransferase terminal-interacting protein 1

MacromoleculeName: Deoxynucleotidyltransferase terminal-interacting protein 1
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.381293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGATGDAEQP RGPSGAERGG LELGDAGAAG QLVLTNPWNI MIKHRQVQRR GRRSQMTTSF TDPAISMDLL RAVLQPSINE EIQTVFNKY MKFFQKAALN VRDNVGEEVD AEQLIQEACR SCLEQAKLLF S

UniProtKB: Deoxynucleotidyltransferase terminal-interacting protein 1

-
Macromolecule #3: Mitotic deacetylase-associated SANT domain protein

MacromoleculeName: Mitotic deacetylase-associated SANT domain protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.794771 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GAVSIEPRIN VGSRFQAEIP LMRDRALAAA DPHKADLVWQ PWEDLESSRE KQRQVEDLLT AACSSIFPGA GTNQELALHC LHESRGDIL ETLNKLLLKK PLRPHNHPLA TYHYTGSDQW KMAERKLFNK GIAIYKKDFF LVQKLIQTKT VAQCVEFYYT Y KKQVKIGR NGTLT

UniProtKB: Mitotic deacetylase-associated SANT domain protein

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #6: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.45 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
12.5 mMHEPES
25.0 mMpotassium acetate
0.25 mMTCEP
0.1 %glutaraldehdye
50.0 mMTris/HCl
GridModel: 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 mA for 30 sec
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 3 sec, blot force 10..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K / Max: 100.0 K
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 129629 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 151434
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 63222
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)

-
Atomic model buiding 1

Initial model
PDB IDChain

5icn

chain_id: B, source_name: PDB, initial_model_type: experimental model

4d6k

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6z2k:
The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more