Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.54 kDa 
• Atom Count: 1392 
• Modelled Residue Count: 162 
• Deposited Residue Count: 173 
• Unique protein chains: 2

2D3G

Double sided ubiquitin binding of Hrs-UIM

• DOI: 10.2210/pdb2D3G/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2005-09-28 Released: 2005-12-20 
• Deposition Author(s): Hirano, S., Kawasaki, M., Kato, R., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.228 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting

Hirano, S., Kawasaki, M., Ura, H., Kato, R., Raiborg, C., Stenmark, H., Wakatsuki, S.

(2006) Nat Struct Mol Biol 13: 272-277

• PubMed: 16462748 
• DOI: 10.1038/nsmb1051
• Primary Citation of Related Structures:  
  2D3G


• PubMed Abstract: 
  

Hrs has an essential role in sorting of monoubiquitinated receptors to multivesicular bodies for lysosomal degradation, through recognition of ubiquitinated receptors by its ubiquitin-interacting motif (UIM). Here, we present the structure of a complex of Hrs-UIM and ubiquitin at 1.7-A resolution. Hrs-UIM forms a single alpha-helix, which binds two ubiquitin molecules, one on either side. These two ubiquitin molecules are related by pseudo two-fold screw symmetry along the helical axis of the UIM, corresponding to a shift by two residues on the UIM helix. Both ubiquitin molecules interact with the UIM in the same manner, using the Ile44 surface, with equal binding affinities. Mutational experiments show that both binding sites of Hrs-UIM are required for efficient degradative protein sorting. Hrs-UIM belongs to a new subclass of double-sided UIMs, in contrast to its yeast homolog Vps27p, which has two tandem single-sided UIMs.

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Organizational Affiliation: 

Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin	A, B	76	Bos taurus	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CH28 (Bos taurus) Explore P0CH28  Go to UniProtKB:  P0CH28

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin interacting motif from hepatocyte growth factor-regulated tyrosine kinase substrate	C [auth P]	21	N/A	Mutation(s): 0
Find proteins for O14964 (Homo sapiens) Explore O14964  Go to UniProtKB:  O14964
NIH Common Fund Data Resources
PHAROS:  O14964 GTEx:  ENSG00000185359

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.228 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.244	α = 90
b = 73.244	β = 90
c = 169.636	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-28 
• Released Date: 2005-12-20 
Deposition Author(s): Hirano, S., Kawasaki, M., Kato, R., Wakatsuki, S.

Revision History  

• Version 1.0: 2005-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance