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 8EBM | pdb_00008ebm

Structure of KLHDC2 substrate binding domain bound to KLHDC2's C-degron mimic

  • 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: 1.58 Å
  • R-Value Free: 
    0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8EBM

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: 82.07 kDa 
  • Atom Count: 5,604 
  • Modeled Residue Count: 661 
  • Deposited Residue Count: 722 
  • 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: KLHDC2, HCA33
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
ASN-GLN-ARG-PHE-GLY-SER-ASN-ASN-THR-SER-GLY-SER
C, D
12Homo sapiensMutation(s): 0 
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.761α = 90
b = 88.634β = 104.57
c = 89.082γ = 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