6XKC | pdb_00006xkc

Crystal structure of E3 ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.242 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6XKC

This is version 1.4 of the entry. See complete history

Literature

Molecular basis for ubiquitin ligase CRL2 FEM1C -mediated recognition of C-degron.

Yan, X.Wang, X.Li, Y.Zhou, M.Li, Y.Song, L.Mi, W.Min, J.Dong, C.

(2021) Nat Chem Biol 17: 263-271

  • DOI: https://doi.org/10.1038/s41589-020-00703-4
  • Primary Citation Related Structures: 
    6XKC, 7JYA

  • PubMed Abstract: 

    Proteome integrity depends on the ubiquitin-proteasome system to degrade unwanted or abnormal proteins. In addition to the N-degrons, C-terminal residues of proteins can also serve as degradation signals (C-degrons) that are recognized by specific cullin-RING ubiquitin ligases (CRLs) for proteasomal degradation. FEM1C is a CRL2 substrate receptor that targets the C-terminal arginine degron (Arg/C-degron), but the molecular mechanism of substrate recognition remains largely elusive. Here, we present crystal structures of FEM1C in complex with Arg/C-degron and show that FEM1C utilizes a semi-open binding pocket to capture the C-terminal arginine and that the extreme C-terminal arginine is the major structural determinant in recognition by FEM1C. Together with biochemical and mutagenesis studies, we provide a framework for understanding molecular recognition of the Arg/C-degron by the FEM family of proteins.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.

Macromolecule Content 

  • Total Structure Weight: 159.75 kDa 
  • Atom Count: 13,062 
  • Modeled Residue Count: 1,458 
  • Deposited Residue Count: 1,476 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein fem-1 homolog C
A, B, C, D, E
A, B, C, D, E, F
246Homo sapiensMutation(s): 0 
Gene Names: FEM1CKIAA1785
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JP0 (Homo sapiens)
Explore Q96JP0 
Go to UniProtKB:  Q96JP0
PHAROS:  Q96JP0
GTEx:  ENSG00000145780 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96JP0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.242 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.003α = 90
b = 97.003β = 90
c = 148.341γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references
  • Version 1.3: 2021-03-10
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Database references, Refinement description