6DO3

KLHDC2 ubiquitin ligase in complex with SelK C-end degron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.165 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kelch domain-containing protein 2
A, B
363Homo sapiensMutation(s): 0 
Gene Names: KLHDC2 (HCA33)
Find proteins for Q9Y2U9 (Homo sapiens)
Go to Gene View: KLHDC2
Go to UniProtKB:  Q9Y2U9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SelK C-end Degron
C, D
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.165 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.816α = 90.00
b = 87.779β = 104.49
c = 88.626γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references