[English] 日本語
Yorodumi
- PDB-6z6h: HDAC-DC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z6h
TitleHDAC-DC
Components
  • (Histone deacetylase HDA1) x 2
  • HDA1 complex subunit 2
  • HDA1 complex subunit 3,HDA1 complex subunit 3
KeywordsGENE REGULATION / Protein complex
Function / homology
Function and homology information


HDA1 complex / Cilium Assembly / negative regulation of transcription by transcription factor localization / HSF1 activation / regulatory ncRNA-mediated gene silencing / histone deacetylase / histone deacetylase activity / histone deacetylase complex / chromosome segregation / chromatin remodeling ...HDA1 complex / Cilium Assembly / negative regulation of transcription by transcription factor localization / HSF1 activation / regulatory ncRNA-mediated gene silencing / histone deacetylase / histone deacetylase activity / histone deacetylase complex / chromosome segregation / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Histone deacetylase class II, yeast / Arb2 domain / HDA1 complex subunit 2/3 / HDA1 complex subunit 3 / HDA1 complex subunit 2/3 superfamily / Arb2 domain / Class II histone deacetylase complex subunits 2 and 3 / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily ...Histone deacetylase class II, yeast / Arb2 domain / HDA1 complex subunit 2/3 / HDA1 complex subunit 3 / HDA1 complex subunit 2/3 superfamily / Arb2 domain / Class II histone deacetylase complex subunits 2 and 3 / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Histone deacetylase HDA1 / HDA1 complex subunit 3 / HDA1 complex subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.55 Å
AuthorsLee, J.-H. / Bollschweiler, D. / Schaefer, T. / Huber, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Sci Adv / Year: 2021
Title: Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies.
Authors: Jung-Hoon Lee / Daniel Bollschweiler / Tillman Schäfer / Robert Huber /
Abstract: The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup ...The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo-electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda1-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification.
History
DepositionMay 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11094
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone deacetylase HDA1
B: Histone deacetylase HDA1
C: HDA1 complex subunit 2
D: HDA1 complex subunit 3,HDA1 complex subunit 3
F: Histone deacetylase HDA1
G: Histone deacetylase HDA1
I: HDA1 complex subunit 2
J: HDA1 complex subunit 3,HDA1 complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)572,67512
Polymers572,4138
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, BS3-crosslinking
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Histone deacetylase HDA1


Mass: 74851.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HDA1, YNL021W, N2819 / Production host: Escherichia coli (E. coli) / References: UniProt: P53973, histone deacetylase
#2: Protein Histone deacetylase HDA1


Mass: 76017.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HDA1, YNL021W, N2819 / Production host: Escherichia coli (E. coli) / References: UniProt: P53973, histone deacetylase
#3: Protein HDA1 complex subunit 2 / Histone deacetylase complex 1 subunit 2


Mass: 71915.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HDA2, PLO2, YDR295C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06629
#4: Protein HDA1 complex subunit 3,HDA1 complex subunit 3 / Histone deacetylase complex 1 subunit 3


Mass: 63422.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HDA3, PLO1, YPR179C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06623
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: HDAC-DC / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
9PHENIXmodel refinement
13cryoSPARC23D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 8.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11396 / Symmetry type: POINT
Atomic model buildingDetails: Real space refinement
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 739.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009339204
ELECTRON MICROSCOPYf_angle_d1.591153000
ELECTRON MICROSCOPYf_chiral_restr0.08665922
ELECTRON MICROSCOPYf_plane_restr0.00946810
ELECTRON MICROSCOPYf_dihedral_angle_d16.38114826

+
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