Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.19 kDa 
• Atom Count: 3321 
• Modelled Residue Count: 469 
• Deposited Residue Count: 732 
• Unique protein chains: 2

3PHD

Crystal structure of human HDAC6 in complex with ubiquitin

• PDB DOI: 10.2210/pdb3PHD/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-11-03 Released: 2011-02-23 
• Deposition Author(s): Dong, A., Qui, W., Ravichandran, M., Schuetz, A., Loppnau, P., Li, F., Mackenzie, F., Kozieradzki, I., Ouyang, H., Structural Genomics Consortium (SGC)

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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 

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

• PubMed: 22069321 
• 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 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.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 6	A, B, C, D	107	Homo sapiens	Mutation(s): 0  Gene Names: HDAC6, KIAA0901, JM21 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBN7 (Homo sapiens) Explore Q9UBN7  Go to UniProtKB:  Q9UBN7
PHAROS:  Q9UBN7 GTEx:  ENSG00000094631

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin	E, F, G, H	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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 = 133.748	α = 90
b = 133.748	β = 90
c = 118.768	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
BUSTER	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-03 
• Released Date: 2011-02-23 
Deposition Author(s): Dong, A., Qui, W., Ravichandran, M., Schuetz, A., Loppnau, P., Li, F., Mackenzie, F., Kozieradzki, I., Ouyang, H., Structural Genomics Consortium (SGC)

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