2V2L

Mutant (E53,56,57,60Q) recombinant horse spleen apoferritin cocrystallized with haemin in acidic conditions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Analysis of Haemin Demetallation by L-Chain Apoferritins

De Val, N.Declercq, J.P.Lim, C.K.Crichton, R.R.

(2012) J.Inorg.Biochem. 112: 77

  • DOI: 10.1016/j.jinorgbio.2012.02.031
  • Primary Citation of Related Structures:  2V2I, 2V2J, 2V2M, 2V2N, 2V2O, 2V2P, 2V2R, 2V2S, 2W0O

  • PubMed Abstract: 
  • There are extensive structural similarities between eukaryotic and prokaryotic ferritins. However, there is one essential difference between these two types of ferritins: bacterioferritins contain haem whereas eukaryotic ferritins are considered to b ...

    There are extensive structural similarities between eukaryotic and prokaryotic ferritins. However, there is one essential difference between these two types of ferritins: bacterioferritins contain haem whereas eukaryotic ferritins are considered to be non-haem proteins. In vitro experiments had shown that horse spleen apoferritin or recombinant horse L chain apoferritins, when co-crystallised with haemin, undergoes demetallation of the porphyrin. In the present study a cofactor has been isolated directly from horse spleen apoferritin and from crystals of the mutant horse L chain apoferritin (E53Q, E56Q, E57Q, E60Q and R59M) which had been co-crystallised with haemin. In both cases the HPLC/ESI-MS results confirm that the cofactor is a N-ethylprotoporphyrin IX. Crystal structures of wild type L chain horse apoferritin and its three mutants co-crystallised with haemin have been determined to high resolution and in all cases a metal-free molecule derived from haemin was found in the hydrophobic pocket, close to the two-fold axis. The X-ray structure of the E53Q, E56Q, E57Q, E60Q+R59M recombinant horse L-chain apoferritin has been obtained at a higher resolution (1.16Å) than previously reported for any mammalian apoferritins. Similar evidence for a metal-free molecule derived from haemin was found in the electron density map of horse spleen apoferritin (at a resolution of 1.5Å). The out-of-plane distortion of the observed porphyrin is clearly compatible with an N-alkyl porphyrin. We conclude that L-chain ferritins are capable of binding and demetallating haemin, generating in the process N-ethylprotoporphyrin IX both in vivo and in vitro.


    Organizational Affiliation

    Institute of Life Sciences, University of Louvain, Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium. natalia.de-val@pasteur.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERRITIN LIGHT CHAIN
A
174Equus caballusGene Names: FTL
Find proteins for P02791 (Equus caballus)
Go to Gene View: FTL
Go to UniProtKB:  P02791
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 182.455α = 90.00
b = 182.455β = 90.00
c = 182.455γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2012-05-16
    Type: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2012-05-30
    Type: Other