6LDP

Structure of CDK5R1-bound FEM1C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Molecular basis for arginine C-terminal degron recognition by Cul2 FEM1 E3 ligase.

Chen, X., Liao, S., Makaros, Y., Guo, Q., Zhu, Z., Krizelman, R., Dahan, K., Tu, X., Yao, X., Koren, I., Xu, C.

(2021) Nat Chem Biol 17: 254-262

  • DOI: 10.1038/s41589-020-00704-3
  • Primary Citation of Related Structures:  
    6LBF, 6LBG, 6LBN, 6LDP, 6LE6, 6LEN, 6LEY, 6LF0, 7CNG

  • PubMed Abstract: 

    • Degrons are elements within protein substrates that mediate the interaction with specific degradation machineries to control proteolysis. Recently, a few classes of C-terminal degrons (C-degrons) that are recognized by dedicated cullin-RING ligases (CRLs) have been identified ...

    Degrons are elements within protein substrates that mediate the interaction with specific degradation machineries to control proteolysis. Recently, a few classes of C-terminal degrons (C-degrons) that are recognized by dedicated cullin-RING ligases (CRLs) have been identified. Specifically, CRL2 using the related substrate adapters FEM1A/B/C was found to recognize C degrons ending with arginine (Arg/C-degron). Here, we uncover the molecular mechanism of Arg/C-degron recognition by solving a subset of structures of FEM1 proteins in complex with Arg/C-degron-bearing substrates. Our structural research, complemented by binding assays and global protein stability (GPS) analyses, demonstrates that FEM1A/C and FEM1B selectively target distinct classes of Arg/C-degrons. Overall, our study not only sheds light on the molecular mechanism underlying Arg/C-degron recognition for precise control of substrate turnover, but also provides valuable information for development of chemical probes for selectively regulating proteostasis.

    Organizational Affiliation: 

    MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China. xuchaor@ustc.edu.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1A, B418Homo sapiensMutation(s): 0 
Gene Names: FEM1C, KIAA1785, CDK5R1, CDK5R, NCK5A
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JP0 (Homo sapiens)
Explore Q96JP0 
Go to UniProtKB:  Q96JP0
PHAROS:  Q96JP0
GTEx:  ENSG00000145780 
Find proteins for Q15078 (Homo sapiens)
Explore Q15078 
Go to UniProtKB:  Q15078
PHAROS:  Q15078
GTEx:  ENSG00000176749 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ96JP0Q15078
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.93α = 90
b = 96.62β = 90
c = 146.52γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references
  • Version 1.3: 2021-03-10
    Changes: Database references