4BKX

The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Class I Hdacs Share a Common Mechanism of Regulation by Inositol Phosphates.

Millard, C.J.Watson, P.J.Celardo, I.Gordiyenko, Y.Cowley, S.M.Robinson, C.V.Fairall, L.Schwabe, J.W.R.

(2013) Mol.Cell 51: 57

  • DOI: 10.1016/j.molcel.2013.05.020

  • PubMed Abstract: 
  • Class I histone deacetylases (HDAC1, HDAC2, and HDAC3) are recruited by cognate corepressor proteins into specific transcriptional repression complexes that target HDAC activity to chromatin resulting in chromatin condensation and transcriptional sil ...

    Class I histone deacetylases (HDAC1, HDAC2, and HDAC3) are recruited by cognate corepressor proteins into specific transcriptional repression complexes that target HDAC activity to chromatin resulting in chromatin condensation and transcriptional silencing. We previously reported the structure of HDAC3 in complex with the SMRT corepressor. This structure revealed the presence of inositol-tetraphosphate [Ins(1,4,5,6)P4] at the interface of the two proteins. It was previously unclear whether the role of Ins(1,4,5,6)P4 is to act as a structural cofactor or a regulator of HDAC3 activity. Here we report the structure of HDAC1 in complex with MTA1 from the NuRD complex. The ELM2-SANT domains from MTA1 wrap completely around HDAC1 occupying both sides of the active site such that the adjacent BAH domain is ideally positioned to recruit nucleosomes to the active site of the enzyme. Functional assays of both the HDAC1 and HDAC3 complexes reveal that Ins(1,4,5,6)P4 is a bona fide conserved regulator of class I HDAC complexes.


    Organizational Affiliation

    Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METASTASIS-ASSOCIATED PROTEIN MTA1
A
176Homo sapiensMutation(s): 0 
Gene Names: MTA1
Find proteins for Q13330 (Homo sapiens)
Go to Gene View: MTA1
Go to UniProtKB:  Q13330
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE DEACETYLASE 1
B
482Homo sapiensMutation(s): 0 
Gene Names: HDAC1 (RPD3L1)
EC: 3.5.1.98
Find proteins for Q13547 (Homo sapiens)
Go to Gene View: HDAC1
Go to UniProtKB:  Q13547
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.199α = 90.00
b = 108.199β = 90.00
c = 133.164γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references