8ZUH | pdb_00008zuh

Crystal structure of bovine Fbs2/Skp1/Man3GlcNAc2 complex

• PDB DOI: https://doi.org/10.2210/pdb8ZUH/pdb

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


• Deposited: 2024-06-09 Released: 2024-09-04 
• Deposition Author(s): Satoh, T., Mizushima, T., Yagi, H., Kato, R., Kato, K.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Models: in silico, experimental

Literature

Structural basis of sugar recognition by SCF FBS2 ubiquitin ligase involved in NGLY1 deficiency.

Satoh, T., Yagi-Utsumi, M., Ishii, N., Mizushima, T., Yagi, H., Kato, R., Tachida, Y., Tateno, H., Matsuo, I., Kato, K., Suzuki, T., Yoshida, Y.

(2024) FEBS Lett 598: 2259-2268

• PubMed: 39171510 
• DOI: https://doi.org/10.1002/1873-3468.15003
• Primary Citation Related Structures: 
  8ZUH


• PubMed Abstract: 
  

  The cytosolic peptide:N-glycanase (PNGase) is involved in the quality control of N-glycoproteins via the endoplasmic reticulum-associated degradation (ERAD) pathway. Mutations in the gene encoding cytosolic PNGase (NGLY1 in humans) cause NGLY1 deficiency. Recent findings indicate that the F-box protein FBS2 of the SCF ^FBS2 ubiquitin ligase complex can be a promising drug target for NGLY1 deficiency. Here, we determined the crystal structure of bovine FBS2 complexed with the adaptor protein SKP1 and a sugar ligand, Man ₃ GlcNAc ₂ , which corresponds to the core pentasaccharide of N-glycan. Our crystallographic data together with NMR data revealed the structural basis of disparate sugar-binding specificities in homologous FBS proteins and identified a potential druggable pocket for in silico docking studies. Our results provide a potential basis for the development of selective inhibitors against FBS2 in NGLY1 deficiency.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan.
Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.
Graduate School of Science and Technology, Gunma University, Kiryu, Japan.
Department of Life Science, Graduate School of Science, University of Hyogo, Himeji, Japan.
Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.
Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Japan.
Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan.
Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 82.41 kDa 
• Atom Count: 5,325 
• Modeled Residue Count: 633 
• Deposited Residue Count: 696 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box only protein 6	A, C	265	Bos taurus	Mutation(s): 0  Gene Names: FBXO6, FBS2, FBX6
UniProt
Find proteins for Q3SX24 (Bos taurus) Explore Q3SX24  Go to UniProtKB:  Q3SX24

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S-phase kinase-associated protein 1	B	166	Bos taurus	Mutation(s): 0  Gene Names: SKP1, SKP1A
UniProt
Find proteins for Q3ZCF3 (Bos taurus) Explore Q3ZCF3  Go to UniProtKB:  Q3ZCF3

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	5		N/A
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.72	α = 90
b = 115.72	β = 90
c = 110.384	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Satoh, T., Mizushima, T., Yagi, H., Kato, R., Kato, K.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP24gm1410003

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Database references, Structure summary