Macromolecule Content

• Total Structure Weight: 21.36 kDa 
• Atom Count: 1497 
• Residue Count: 185 
• Unique protein chains: 2

2Z59

Complex Structures of Mouse Rpn13 (22-130aa) and ubiquitin

• DOI: 10.2210/pdb2Z59/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-01 Released: 2008-05-20 
• Deposition Author(s): Chen, X., Schreiner, P., Groll, M., Walters, K.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction.

Schreiner, P., Chen, X., Husnjak, K., Randles, L., Zhang, N., Elsasser, S., Finley, D., Dikic, I., Walters, K.J., Groll, M.

(2008) Nature 453: 548-552

• PubMed: 18497827 
• DOI: 10.1038/nature06924
• Primary Citation of Related Structures:  
  2R2Y, 2Z59


• PubMed Abstract: 
  

Targeted protein degradation is largely performed by the ubiquitin-proteasome pathway, in which substrate proteins are marked by covalently attached ubiquitin chains that mediate recognition by the proteasome. It is currently unclear how the proteasome recognizes its substrates, as the only established ubiquitin receptor intrinsic to the proteasome is Rpn10/S5a (ref. 1), which is not essential for ubiquitin-mediated protein degradation in budding yeast. In the accompanying manuscript we report that Rpn13 (refs 3-7), a component of the nine-subunit proteasome base, functions as a ubiquitin receptor, complementing its known role in docking de-ubiquitinating enzyme Uch37/UCHL5 (refs 4-6) to the proteasome. Here we merge crystallography and NMR data to describe the ubiquitin-binding mechanism of Rpn13. We determine the structure of Rpn13 alone and complexed with ubiquitin. The co-complex reveals a novel ubiquitin-binding mode in which loops rather than secondary structural elements are used to capture ubiquitin. Further support for the role of Rpn13 as a proteasomal ubiquitin receptor is demonstrated by its ability to bind ubiquitin and proteasome subunit Rpn2/S1 simultaneously. Finally, we provide a model structure of Rpn13 complexed to diubiquitin, which provides insights into how Rpn13 as a ubiquitin receptor is coupled to substrate deubiquitination by Uch37.

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Organizational Affiliation: 

Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ADRM1	A	109	Mus musculus	Mutation(s): 0  Gene Names: Adrm1, Gp110
Find proteins for Q9JKV1 (Mus musculus) Explore Q9JKV1  Go to UniProtKB:  Q9JKV1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: Rps27a, Uba80, Ubcep1, UBC
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS:  P0CG48

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2Z59 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-01 
• Released Date: 2008-05-20 
Deposition Author(s): Chen, X., Schreiner, P., Groll, M., Walters, K.J.

Revision History 

• Version 1.0: 2008-05-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance