Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 48.85 kDa 
• Atom Count: 3,221 
• Modelled Residue Count: 391 
• Deposited Residue Count: 421 
• Unique protein chains: 2

 3WSO

Crystal structure of the Skp1-FBG3 complex

• PDB DOI:  https://doi.org/10.2210/pdb3WSO/pdb

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


• Deposited: 2014-03-18 Released: 2015-03-25 
• Deposition Author(s): Kumanomidou, T., Nishio, K., Takagi, K., Nakagawa, T., Suzuki, A., Yamane, T., Tokunaga, F., Iwai, K., Murakami, A., Yoshida, Y., Tanaka, K., Mizushima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.266 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

The Structural Differences between a Glycoprotein Specific F-Box Protein Fbs1 and Its Homologous Protein FBG3

Kumanomidou, T., Nishio, K., Takagi, K., Nakagawa, T., Suzuki, A., Yamane, T., Tokunaga, F., Iwai, K., Murakami, A., Yoshida, Y., Tanaka, K., Mizushima, T.

(2015) PLoS One 10: e0140366-e0140366

• PubMed: 26460611 
• DOI: https://doi.org/10.1371/journal.pone.0140366
• Primary Citation of Related Structures:  
  3WSO


• PubMed Abstract: 
  

The Skp1-Cul1-F-box protein (SCF) complex catalyzes protein ubiquitination in diverse cellular processes and is one of the best-characterized ubiquitin ligases. F-box proteins determine the substrate specificities of SCF ubiquitin ligases. Among these, Fbs1/FBG1/FBXO2, Fbs2/FBG2/FBXO6, and Fbs3/FBG5/FBXO27 recognize the N-glycans of glycoproteins, whereas FBG3/FBXO44 has no sugar-binding activity, despite the high sequence homology and conservation of the residues necessary for oligosaccharide binding between Fbs1-3 and FBG3. Here we determined the crystal structure of the Skp1-FBG3 complex at a resolution of 2.6 Å. The substrate-binding domain of FBG3 is composed of a 10-stranded antiparallel β-sandwich with three helices. Although the overall structure of FBG3 is similar to that of Fbs1, the residues that form the Fbs1 carbohydrate-binding pocket failed to be superposed with the corresponding residues of FBG3. Structure-based mutational analysis shows that distinct hydrogen bond networks of four FBG3 loops, i.e., β2-β3, β5-β6, β7-β8, and β9-β10, prevent the formation of the carbohydrate-binding pocket shown in Fbs1.

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Organizational Affiliation: 

Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box only protein 44	A	255	Homo sapiens	Mutation(s): 0  Gene Names: FBXO44, FBG3, FBX30, FBX44, FBX6A, FBXO6A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4M3 (Homo sapiens) Explore Q9H4M3  Go to UniProtKB:  Q9H4M3
PHAROS:  Q9H4M3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S-phase kinase-associated protein 1	B	166	Homo sapiens	Mutation(s): 0  Gene Names: SKP1, EMC19, OCP2, SKP1A, TCEB1L
UniProt & NIH Common Fund Data Resources
Find proteins for P63208 (Homo sapiens) Explore P63208  Go to UniProtKB:  P63208
PHAROS:  P63208

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.266 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.12	α = 90
b = 76.594	β = 90
c = 193.939	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Kumanomidou, T., Nishio, K., Takagi, K., Nakagawa, T., Suzuki, A., Yamane, T., Tokunaga, F., Iwai, K., Murakami, A., Yoshida, Y., Tanaka, K., Mizushima, T.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2015-11-11
  Changes: Other