5V1Y

Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.421 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism.

VanderLinden, R.T.Hemmis, C.W.Yao, T.Robinson, H.Hill, C.P.

(2017) J. Biol. Chem. 292: 9493-9504

  • DOI: 10.1074/jbc.M117.785287
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 26S proteasome is a large cellular assembly that mediates the selective degradation of proteins in the nucleus and cytosol and is an established target for anticancer therapeutics. Protein substrates are typically targeted to the proteasome throu ...

    The 26S proteasome is a large cellular assembly that mediates the selective degradation of proteins in the nucleus and cytosol and is an established target for anticancer therapeutics. Protein substrates are typically targeted to the proteasome through modification with a polyubiquitin chain, which can be recognized by several proteasome-associated ubiquitin receptors. One of these receptors, RPN13/ADRM1, is recruited to the proteasome through direct interaction with the large scaffolding protein RPN2 within the 19S regulatory particle. To better understand the interactions between RPN13, RPN2, and ubiquitin, we used human proteins to map the RPN13-binding epitope to the C-terminal 14 residues of RPN2, which, like ubiquitin, binds the N-terminal pleckstrin-like receptor of ubiquitin (PRU) domain of RPN13. We also report the crystal structures of the RPN13 PRU domain in complex with peptides corresponding to the RPN2 C terminus and ubiquitin. Through mutational analysis, we validated the RPN2-binding interface revealed by our structures and quantified binding interactions with surface plasmon resonance and fluorescence polarization. In contrast to a previous report, we find that RPN13 binds ubiquitin with an affinity similar to that of other proteasome-associated ubiquitin receptors and that RPN2, ubiquitin, and the deubiquitylase UCH37 bind to RPN13 with independent energetics. These findings provide a detailed characterization of interactions that are important for proteasome function, indicate ubiquitin affinities that are consistent with the role of RPN13 as a proteasomal ubiquitin receptor, and have major implications for the development of novel anticancer therapeutics.


    Organizational Affiliation

    From the Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasomal ubiquitin receptor ADRM1
A, B
115Homo sapiensMutation(s): 0 
Gene Names: ADRM1 (GP110)
Find proteins for Q16186 (Homo sapiens)
Go to Gene View: ADRM1
Go to UniProtKB:  Q16186
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
C, D
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 1
E, F
16Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
Go to Gene View: PSMD1
Go to UniProtKB:  Q99460
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.421 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.129α = 90.00
b = 96.098β = 96.38
c = 57.605γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM059135
National Institutes of Health/National Cancer InstituteUnited StatesR21 CA191929

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-10
    Type: Database references
  • Version 1.2: 2017-06-21
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence