3PHD

Crystal structure of human HDAC6 in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Protein Aggregates Are Recruited to Aggresome by Histone Deacetylase 6 via Unanchored Ubiquitin C Termini.

Ouyang, H.Ali, Y.O.Ravichandran, M.Dong, A.Qiu, W.Mackenzie, F.Dhe-Paganon, S.Arrowsmith, C.H.Zhai, R.G.

(2012) J.Biol.Chem. 287: 2317-2327

  • DOI: 10.1074/jbc.M111.273730

  • PubMed Abstract: 
  • The aggresome pathway is activated when proteasomal clearance of misfolded proteins is hindered. Misfolded polyubiquitinated protein aggregates are recruited and transported to the aggresome via the microtubule network by a protein complex consisting ...

    The aggresome pathway is activated when proteasomal clearance of misfolded proteins is hindered. Misfolded polyubiquitinated protein aggregates are recruited and transported to the aggresome via the microtubule network by a protein complex consisting of histone deacetylase 6 (HDAC6) and the dynein motor complex. The current model suggests that HDAC6 recognizes protein aggregates by binding directly to polyubiquitinated proteins. Here, we show that there are substantial amounts of unanchored ubiquitin in protein aggregates with solvent-accessible C termini. The ubiquitin-binding domain (ZnF-UBP) of HDAC6 binds exclusively to the unanchored C-terminal diglycine motif of ubiquitin instead of conjugated polyubiquitin. The unanchored ubiquitin C termini in the aggregates are generated in situ by aggregate-associated deubiquitinase ataxin-3. These results provide structural and mechanistic bases for the role of HDAC6 in aggresome formation and further suggest a novel ubiquitin-mediated signaling pathway, where the exposure of ubiquitin C termini within protein aggregates enables HDAC6 recognition and transport to the aggresome.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada. hui.ouyang@utoronto.ca




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 6
A, B, C, D
107Homo sapiensMutation(s): 0 
Gene Names: HDAC6 (KIAA0901)
EC: 3.5.1.98
Find proteins for Q9UBN7 (Homo sapiens)
Go to Gene View: HDAC6
Go to UniProtKB:  Q9UBN7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin
E, F, G, H
76Homo sapiensMutation(s): 0 
Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
Go to Gene View: UBA52
Go to UniProtKB:  P62987
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 133.748α = 90.00
b = 133.748β = 90.00
c = 118.768γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-16
    Type: Database references
  • Version 1.3: 2011-11-23
    Type: Database references
  • Version 1.4: 2012-02-08
    Type: Database references