2N3T | pdb_00002n3t

Solution structure of the Rpn1 substrate receptor site toroid 1 (T1)

• PDB DOI: https://doi.org/10.2210/pdb2N3T/pdb
• BMRB: 25657

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-10 Released: 2016-02-24 
• Deposition Author(s): Chen, X., Walters, K.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome.

Shi, Y., Chen, X., Elsasser, S., Stocks, B.B., Tian, G., Lee, B.H., Shi, Y., Zhang, N., de Poot, S.A., Tuebing, F., Sun, S., Vannoy, J., Tarasov, S.G., Engen, J.R., Finley, D., Walters, K.J.

(2016) Science 351

• PubMed: 26912900 
• DOI: https://doi.org/10.1126/science.aad9421
• Primary Citation Related Structures: 
  2N3T, 2N3U, 2N3V, 2N3W


• PubMed Abstract: 
  

  Hundreds of pathways for degradation converge at ubiquitin recognition by a proteasome. Here, we found that the five known proteasomal ubiquitin receptors in yeast are collectively nonessential for ubiquitin recognition and identified a sixth receptor, Rpn1. A site ( T1: ) in the Rpn1 toroid recognized ubiquitin and ubiquitin-like ( UBL: ) domains of substrate shuttling factors. T1 structures with monoubiquitin or lysine 48 diubiquitin show three neighboring outer helices engaging two ubiquitins. T1 contributes a distinct substrate-binding pathway with preference for lysine 48-linked chains. Proximal to T1 within the Rpn1 toroid is a second UBL-binding site ( T2: ) that assists in ubiquitin chain disassembly, by binding the UBL of deubiquitinating enzyme Ubp6. Thus, a two-site recognition domain intrinsic to the proteasome uses distinct ubiquitin-fold ligands to assemble substrates, shuttling factors, and a deubiquitinating enzyme.

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Organizational Affiliation: 
• Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.
Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.
Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Linganore High School, Frederick, MD 21701, USA.
Biophysics Resource, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA. [e-mail] [e-mail] [e-mail].
Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. [e-mail] [e-mail] [e-mail].
Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.64 kDa 
• Atom Count: 954 
• Modeled Residue Count: 131 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN1	A	131	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN1, HRD2, NAS1, RPD1, YHR027C
UniProt
Find proteins for P38764 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38764  Go to UniProtKB:  P38764

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Chen, X., Walters, K.J.

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references