3V5X

Structure of FBXL5 hemerythrin domain, C2 cell


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Molecular Characterization of Iron-sensing Hemerythrin-like Domain within F-box and Leucine-rich Repeat Protein 5 (FBXL5).

Thompson, J.W.Salahudeen, A.A.Chollangi, S.Ruiz, J.C.Brautigam, C.A.Makris, T.M.Lipscomb, J.D.Tomchick, D.R.Bruick, R.K.

(2012) J.Biol.Chem. 287: 7357-7365

  • DOI: 10.1074/jbc.M111.308684
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mammalian cells maintain iron homeostasis by sensing changes in bioavailable iron levels and promoting adaptive responses. FBXL5 is a subunit of an E3 ubiquitin ligase complex that mediates the stability of iron regulatory protein 2, an important pos ...

    Mammalian cells maintain iron homeostasis by sensing changes in bioavailable iron levels and promoting adaptive responses. FBXL5 is a subunit of an E3 ubiquitin ligase complex that mediates the stability of iron regulatory protein 2, an important posttranscriptional regulator of several genes involved in iron metabolism. The stability of FBXL5 is regulated in an iron- and oxygen-responsive manner, contingent upon the presence of its N-terminal domain. Here we present the atomic structure of the FBXL5 N terminus, a hemerythrin-like α-helical bundle fold not previously observed in mammalian proteins. The core of this domain employs an unusual assortment of amino acids necessary for the assembly and sensing properties of its diiron center. These regulatory features govern the accessibility of a mapped sequence required for proteasomal degradation of FBXL5. Detailed molecular and structural characterization of the ligand-responsive hemerythrin domain provides insights into the mechanisms by which FBXL5 serves as a unique mammalian metabolic sensor.


    Related Citations: 
    • An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis.
      Salahudeen, A.A.,Thompson, J.W.,Ruiz, J.C.,Ma, H.W.,Kinch, L.N.,Li, Q.,Grishin, N.V.,Bruick, R.K.
      (2009) Science 326: 722


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
F-box/LRR-repeat protein 5
A, B
161Homo sapiensMutation(s): 0 
Gene Names: FBXL5 (FBL4, FBL5, FLR1)
Find proteins for Q9UKA1 (Homo sapiens)
Go to Gene View: FBXL5
Go to UniProtKB:  Q9UKA1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEO
Query on FEO

Download SDF File 
Download CCD File 
A, B
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.118α = 90.00
b = 75.802β = 111.75
c = 78.727γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
SHELXDphasing
PHENIXrefinement
SBC-Collectdata collection
HKL-3000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references
  • Version 1.2: 2012-03-21
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description