2N3T

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1126/science.aad9421
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN1131Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN1HRD2NAS1RPD1YHR027C
UniProt
Find proteins for P38764 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38764 
Go to UniProtKB:  P38764
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38764
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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