8EBL | pdb_00008ebl

Structure of KLHDC2 substrate binding domain bound to C-degron from EPHB2

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-08-31 Released: 2023-02-22 
  • Deposition Author(s): Scott, D.C., Schulman, B.A.
  • Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8EBL

This is version 1.2 of the entry. See complete history

Literature

E3 ligase autoinhibition by C-degron mimicry maintains C-degron substrate fidelity.

Scott, D.C.King, M.T.Baek, K.Gee, C.T.Kalathur, R.Li, J.Purser, N.Nourse, A.Chai, S.C.Vaithiyalingam, S.Chen, T.Lee, R.E.Elledge, S.J.Kleiger, G.Schulman, B.A.

(2023) Mol Cell 83: 770-786.e9

  • DOI: https://doi.org/10.1016/j.molcel.2023.01.019
  • Primary Citation Related Structures: 
    8EBL, 8EBM, 8EBN

  • PubMed Abstract: 

    E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins with terminal degron-like sequences remains unclear. Here, we report that human KLHDC2, a CRL2 substrate receptor targeting C-terminal Gly-Gly degrons, is regulated through interconversion between two assemblies. In the self-inactivated homotetramer, KLHDC2's C-terminal Gly-Ser motif mimics a degron and engages the substrate-binding domain of another protomer. True substrates capture the monomeric CRL2 KLHDC2 , driving E3 activation by neddylation and subsequent substrate ubiquitylation. Non-substrates such as NEDD8 bind KLHDC2 with high affinity, but its slow on rate prevents productive association with CRL2 KLHDC2 . Without substrate, neddylated CRL2 KLHDC2 assemblies are deactivated via distinct mechanisms: the monomer by deneddylation and the tetramer by auto-ubiquitylation. Thus, substrate specificity is amplified by KLHDC2 self-assembly acting like a molecular timer, where only bona fide substrates may bind before E3 ligase inactivation.


  • Organizational Affiliation
    • Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. Electronic address: danny.scott@stjude.org.

Macromolecule Content 

  • Total Structure Weight: 82.47 kDa 
  • Atom Count: 5,988 
  • Modeled Residue Count: 682 
  • Deposited Residue Count: 726 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kelch domain-containing protein 2
A, B
349Homo sapiensMutation(s): 0 
Gene Names: KLHDC2HCA33
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2U9 (Homo sapiens)
Explore Q9Y2U9 
Go to UniProtKB:  Q9Y2U9
PHAROS:  Q9Y2U9
GTEx:  ENSG00000165516 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2U9
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GLU-ASP-SER-HIS-LYS-GLU-SER-ASN-ASP-CYS-SER-CYS-GLY-GLYC [auth D],
D [auth C]
14Homo sapiensMutation(s): 0 
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29323 (Homo sapiens)
Explore P29323 
Go to UniProtKB:  P29323
PHAROS:  P29323
GTEx:  ENSG00000133216 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29323
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.48α = 90
b = 84.482β = 90
c = 90.729γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesR01GM125885
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesP30CA021765

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Refinement description