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 A, B363Homo sapiensMutation(s): 0 
Gene Names: KLHDC2, HCA33
Find proteins for Q9Y2U9 (Homo sapiens)
Explore Q9Y2U9 
Go to UniProtKB:  Q9Y2U9
NIH Common Fund Data Resources
PHAROS:  Q9Y2U9
GTEx:  ENSG00000165516
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
USP1 C-END DEGRON C, D6Homo 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
GTEx:  ENSG00000162607
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


View more in-depth experimental data

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