Macromolecule Content

• Total Structure Weight: 13.26 kDa 
• Atom Count: 929 
• Residue Count: 119 
• Unique protein chains: 2

2G3Q

Solution Structure of Ede1 UBA-ubiquitin complex

• DOI: 10.2210/pdb2G3Q/pdb
• BMRB: 7002

• Classification: ENDOCYTOSIS/SIGNALING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-02-20 Released: 2006-05-09 
• Deposition Author(s): Swanson, K.A., Hicke, L., Radhakrishnan, I.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 20 
• Selection Criteria: The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry 

Literature

Structural Basis for Monoubiquitin Recognition by the Ede1 UBA Domain.

Swanson, K.A., Hicke, L., Radhakrishnan, I.

(2006) J Mol Biol 358: 713-724

• PubMed: 16563434 
• DOI: 10.1016/j.jmb.2006.02.059
• Primary Citation of Related Structures:  
  2G3Q


• PubMed Abstract: 
  

Monoubiquitination is a general mechanism for downregulating the activity of cell surface receptors by consigning these proteins for lysosome-mediated degradation through the endocytic pathway. The yeast Ede1 protein functions at the internalization step of endocytosis and binds monoubiquitinated proteins through a ubiquitin associated (UBA) domain. UBA domains are found in a broad range of cellular proteins but previous studies have suggested that the mode of ubiquitin recognition might not be universally conserved. Here we present the solution structure of the Ede1 UBA domain in complex with monoubiquitin. The Ede1 UBA domain forms a three-helix bundle structure and binds ubiquitin through a largely hydrophobic surface in a manner reminiscent of the Dsk2 UBA and the remotely homologous Cue2 CUE domains, for which high-resolution structures have been described. However, the interaction is dissimilar to the molecular models proposed for the hHR23A UBA domains bound to either monoubiquitin or Lys48-linked diubiquitin. Our mutational analyses of the Ede1 UBA domain-ubiquitin interaction reveal several key affinity determinants and, unexpectedly, a negative affinity determinant in the wild-type Ede1 protein, implying that high-affinity interactions may not be the sole criterion for optimal function of monoubiquitin-binding endocytic proteins.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, 2-100 Hogan Bldg, Evanston, IL 60208-3500, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein YBL047C	A	43	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: EDE1
Find proteins for P34216 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34216  Go to UniProtKB:  P34216

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CG63 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CG63  Go to UniProtKB:  P0CG63

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 20 
• Selection Criteria: The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry 
• OLDERADO: 2G3Q Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-20 
• Released Date: 2006-05-09 
Deposition Author(s): Swanson, K.A., Hicke, L., Radhakrishnan, I.

Revision History 

• Version 1.0: 2006-05-09
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance