Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 159.75 kDa 
• Atom Count: 13062 
• Modelled Residue Count: 1458 
• Deposited Residue Count: 1476 
• Unique protein chains: 1

6XKC

Crystal structure of E3 ligase

• DOI: 10.2210/pdb6XKC/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-06-26 Released: 2020-10-14 
• Deposition Author(s): Yan, X., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Min, J.R., Dong, C., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.242 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

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

• PubMed: 33398170 
• DOI: 10.1038/s41589-020-00703-4
• Primary Citation of 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.

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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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein fem-1 homolog C	A, B, C, D, E, F	246	Homo sapiens	Mutation(s): 0  Gene Names: FEM1C, KIAA1785
Find proteins for Q96JP0 (Homo sapiens) Explore Q96JP0  Go to UniProtKB:  Q96JP0
NIH Common Fund Data Resources
PHAROS:  Q96JP0 GTEx:  ENSG00000145780

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.242 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.003	α = 90
b = 97.003	β = 90
c = 148.341	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-06-26 
• Released Date: 2020-10-14 
Deposition Author(s): Yan, X., Dong, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Min, J.R., Dong, C., Structural Genomics Consortium (SGC)

Revision History  

• 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