Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.65 kDa 
• Atom Count: 1410 
• Modelled Residue Count: 172 
• Deposited Residue Count: 215 
• Unique protein chains: 2

2DX5

The complex structure between the mouse EAP45-GLUE domain and ubiquitin

• PDB DOI: 10.2210/pdb2DX5/pdb

• Classification: PROTEIN TRANSPORT/SIGNALING PROTEIN
• Organism(s): Mus musculus, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-24 Released: 2006-10-10 
• Deposition Author(s): Hirano, S., Suzuki, N., Slagsvold, T., Kawasaki, M., Trambaiolo, D., Kato, R., Stenmark, H., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.329 
• R-Value Work: 0.285 
• R-Value Observed: 0.285 

Literature

Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain

Hirano, S., Suzuki, N., Slagsvold, T., Kawasaki, M., Trambaiolo, D., Kato, R., Stenmark, H., Wakatsuki, S.

(2006) Nat Struct Mol Biol 13: 1031-1032

• PubMed: 17057714 
• DOI: 10.1038/nsmb1163
• Primary Citation of Related Structures:  
  2DX5


• PubMed Abstract: 
  

ESCRT-II, a complex that sorts ubiquitinated membrane proteins to lysosomes, localizes to endosomes through interaction between the Vps36 subunit's GLUE domain and phosphatidylinositides (PIs). In yeast, a ubiquitin (Ub)-interacting NZF domain is inserted in Vps36 GLUE, whereas its mammalian counterpart, Eap45 GLUE, lacks the NZF domain. In the Eap45 GLUE-Ub complex structure, Ub binds far from the proposed PI-binding site of Eap45 GLUE, suggesting their independent binding.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting protein 36	A	139	Mus musculus	Mutation(s): 0  Gene Names: Vps36
UniProt & NIH Common Fund Data Resources
Find proteins for Q91XD6 (Mus musculus) Explore Q91XD6  Go to UniProtKB:  Q91XD6
IMPC:  MGI:1917410

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Bos taurus	Mutation(s): 0  Gene Names: UBC
UniProt
Find proteins for P0CH28 (Bos taurus) Explore P0CH28  Go to UniProtKB:  P0CH28

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.329 
• R-Value Work: 0.285 
• R-Value Observed: 0.285 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.82	α = 90
b = 87.82	β = 90
c = 49.708	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-24 
• Released Date: 2006-10-10 
Deposition Author(s): Hirano, S., Suzuki, N., Slagsvold, T., Kawasaki, M., Trambaiolo, D., Kato, R., Stenmark, H., Wakatsuki, S.

Revision History  

• Version 1.0: 2006-10-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance