6DO5

KLHDC2 ubiquitin ligase in complex with USP1 C-end degron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of the Diglycine C-End Degron by CRL2KLHDC2Ubiquitin Ligase.

Rusnac, D.V.Lin, H.C.Canzani, D.Tien, K.X.Hinds, T.R.Tsue, A.F.Bush, M.F.Yen, H.S.Zheng, N.

(2018) Mol Cell 72: 813-822.e4

  • DOI: 10.1016/j.molcel.2018.10.021
  • Primary Citation of Related Structures:  
    6DO4, 6DO3, 6DO5

  • PubMed Abstract: 
  • Aberrant proteins can be deleterious to cells and are cleared by the ubiquitin-proteasome system. A group of C-end degrons that are recognized by specific cullin-RING ubiquitin E3 ligases (CRLs) has recently been identified in some of these abnormal poly ...

    Aberrant proteins can be deleterious to cells and are cleared by the ubiquitin-proteasome system. A group of C-end degrons that are recognized by specific cullin-RING ubiquitin E3 ligases (CRLs) has recently been identified in some of these abnormal polypeptides. Here, we report three crystal structures of a CRL2 substrate receptor, KLHDC2, in complex with the diglycine-ending C-end degrons of two early-terminated selenoproteins and the N-terminal proteolytic fragment of USP1. The E3 recognizes the degron peptides in a similarly coiled conformation and cradles their C-terminal diglycine with a deep surface pocket. By hydrogen bonding with multiple backbone carbonyls of the peptides, KLHDC2 further locks in the otherwise degenerate degrons with a compact interface and unexpected high affinities. Our results reveal the structural mechanism by which KLHDC2 recognizes the simplest C-end degron and suggest a functional necessity of the E3 to tightly maintain the low abundance of its select substrates.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA. Electronic address: nzheng@uw.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kelch domain-containing protein 2 AB363Homo sapiensMutation(s): 0 
Gene Names: KLHDC2HCA33
Find proteins for Q9Y2U9 (Homo sapiens)
Explore Q9Y2U9 
Go to UniProtKB:  Q9Y2U9
NIH Common Fund Data Resources
PHAROS:  Q9Y2U9
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
USP1 C-END DEGRON CD6Homo sapiensMutation(s): 0 
Gene Names: USP1
EC: 3.4.19.12
Find proteins for O94782 (Homo sapiens)
Explore O94782 
Go to UniProtKB:  O94782
NIH Common Fund Data Resources
PHAROS:  O94782
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.496α = 90
b = 87.086β = 104.56
c = 88.322γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence