6OI4

RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Phosphorylation of Tyr-950 in the proteasome scaffolding protein RPN2 modulates its interaction with the ubiquitin receptor RPN13.

Hemmis, C.W.Heard, S.C.Hill, C.P.

(2019) J Biol Chem 294: 9659-9665

  • DOI: 10.1074/jbc.AC119.008881
  • Primary Citation of Related Structures:  
    6OI4

  • PubMed Abstract: 
  • Protein substrates are targeted to the 26S proteasome through several ubiquitin receptors. One of these receptors, RPN13, is recruited to the proteasome by binding of its N-terminal pleckstrin-like receptor of ubiquitin (PRU) domain to C-terminal res ...

    Protein substrates are targeted to the 26S proteasome through several ubiquitin receptors. One of these receptors, RPN13, is recruited to the proteasome by binding of its N-terminal pleckstrin-like receptor of ubiquitin (PRU) domain to C-terminal residues of the scaffolding protein RPN2. The RPN13 PRU domain is followed by a flexible linker and a C-terminal deubiquitylase adaptor (DEUBAD) domain, which recruits and activates the deubiquitylase UCH37. Both RPN13 and UCH37 have been implicated in human cancers, and inhibitors of the RPN2-RPN13 interaction are being developed as potential therapeutic anticancer agents. Our current study builds on the recognition that a residue central to the RPN2-RPN13 interaction, RPN2 Tyr-950, is phosphorylated in Jurkat cells. We found that the Tyr-950 phosphorylation enhances binding to RPN13. The crystal structure of the RPN2-RPN13 pTyr-950-ubiquitin complex was determined at 1.76-Å resolution and reveals specific interactions with positively charged side chains in RPN13 that explain how phosphorylation increases binding affinity without inducing conformational change. Mutagenesis and quantitative binding assays were then used to validate the crystallographic interface. Our findings support a model in which RPN13 recruitment to the proteasome is enhanced by phosphorylation of RPN2 Tyr-950, have important implications for efforts to develop specific inhibitors of the RPN2-RPN13 interaction, and suggest the existence of a previously unknown stress-response pathway.


    Organizational Affiliation

    From the Departments of Biochemistry and chris@biochem.utah.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasomal ubiquitin receptor ADRM1AB113Homo sapiensMutation(s): 0 
Gene Names: ADRM1GP110
Find proteins for Q16186 (Homo sapiens)
Explore Q16186 
Go to UniProtKB:  Q16186
NIH Common Fund Data Resources
PHAROS  Q16186
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ubiquitinCD76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
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PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1EF14Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
Explore Q99460 
Go to UniProtKB:  Q99460
NIH Common Fund Data Resources
PHAROS  Q99460
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A, C, D, F
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
E,FL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.373α = 90
b = 99.373β = 90
c = 41.705γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Cancer SocietyUnited StatesPF-16-100-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence