2N3W

Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted binding mode


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1126/science.aad9421
  • Primary Citation of Related Structures:  
    2N3V, 2N3U, 2N3T, 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 recepto ...

    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

    Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. j.engen@neu.edu kylie.walters@nih.gov daniel_finley@hms.harvard.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN1A131Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN1HRD2NAS1RPD1YHR027C
Find proteins for P38764 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38764 
Go to UniProtKB:  P38764
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40BC76Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
NIH Common Fund Data Resources
PHAROS  P62987
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • OLDERADO: 2N3W Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references