5HDW

ApaG Domain of FBxo3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure and interaction studies of the human FBxo3 ApaG domain.

Krzysiak, T.C.Chen, B.B.Lear, T.Mallampalli, R.K.Gronenborn, A.M.

(2016) FEBS J 283: 2091-2101

  • DOI: https://doi.org/10.1111/febs.13721
  • Primary Citation of Related Structures:  
    5HDW

  • PubMed Abstract: 

    Transcriptional activation of proinflammatory cytokines, mediated by tumor necrosis factor receptor-associated factors (TRAFs), is in part triggered by the degradation of the F-box protein, FBxl2, via an E3 ligase that contains another F-box protein, FBxo3. The ApaG domain of FBxo3 is required for the interaction with and degradation of FBxl2 [Mallampalli RK et al., (2013) J Immunol 191, 5247-5255]. Here, we report the X-ray structure of the human FBxo3 ApaG domain, residues 278-407, at 2.0 Å resolution. Like bacterial ApaG proteins, this domain is characterized by a classic Immunoglobin/Fibronectin III-type fold, comprising a seven-stranded β-sheet core, surrounded by four extended loops. Although cation binding had been proposed for bacterial ApaG proteins, no interactions with Mg(2+) or Co(2+) were detected for the human ApaG domain. In addition, dinucleotide polyphosphates, which have been reported to be second messengers in the inflammation response and targets of the bacterial apaG-containing operon, are not bound by the human ApaG domain. In the context of the full-length protein, loop 1, comprising residues 294-303, is critical for the interaction with FBxl2. However, titration of the individual ApaG domain with a 15-mer FBxl2 peptide that was phosphorylated on the crucial T404, as well as the inability of the ApaG domain to interact with full-length FBxl2, assessed by coimmunoprecipitation, indicate that the ApaG domain alone is necessary, but not sufficient for binding and degradation of FBxl2. PDB ID (5HDW).


  • Organizational Affiliation

    Department of Structural Biology, Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
F-box only protein 3133Homo sapiensMutation(s): 0 
Gene Names: FBXO3FBX3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK99 (Homo sapiens)
Explore Q9UK99 
Go to UniProtKB:  Q9UK99
PHAROS:  Q9UK99
GTEx:  ENSG00000110429 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UK99
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.477α = 90
b = 96.813β = 90
c = 40.517γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL096376
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL097376
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL098174
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL081784
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesPO1HL114453
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL116472

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description