3PHD

Crystal structure of human HDAC6 in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1074/jbc.M111.273730
  • Primary Citation of Related Structures:  
    3PHD

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 6
A, B, C, D
107Homo sapiensMutation(s): 0 
Gene Names: HDAC6KIAA0901JM21
EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBN7 (Homo sapiens)
Explore Q9UBN7 
Go to UniProtKB:  Q9UBN7
PHAROS:  Q9UBN7
GTEx:  ENSG00000094631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBN7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin
E, F, G, H
76Homo sapiensMutation(s): 0 
Gene Names: UBBUBA52UBCEP2UBCRPS27AUBA80UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth B]
M [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.748α = 90
b = 133.748β = 90
c = 118.768γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
BUSTERrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Database references
  • Version 1.3: 2011-11-23
    Changes: Database references
  • Version 1.4: 2012-02-08
    Changes: Database references
  • Version 1.5: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description