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 1.4 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
  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 6A, B, C, D107Homo sapiensMutation(s): 0 
Gene Names: HDAC6, KIAA0901, JM21
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
Find proteins for Q9UBN7 (Homo sapiens)
Explore Q9UBN7 
Go to UniProtKB:  Q9UBN7
NIH Common Fund Data Resources
PHAROS  Q9UBN7
GTEx  ENSG00000094631
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PolyubiquitinE, F, G, H76Homo sapiensMutation(s): 0 
Gene Names: UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS  P0CG47
Protein Feature View
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  • Reference Sequence
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

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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