2W0O | pdb_00002w0o

Horse spleen apoferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.236 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1016/j.jinorgbio.2012.02.031
  • Primary Citation Related Structures: 
    2V2I, 2V2J, 2V2L, 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 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

Macromolecule Content 

  • Total Structure Weight: 20.76 kDa 
  • Atom Count: 1,616 
  • Modeled Residue Count: 170 
  • Deposited Residue Count: 174 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FERRITIN LIGHT CHAIN174Equus caballusMutation(s): 0 
UniProt
Find proteins for P02791 (Equus caballus)
Explore P02791 
Go to UniProtKB:  P02791
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02791
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD

Query on CD



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182α = 90
b = 182β = 90
c = 182γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2012-05-16
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2012-05-30
    Changes: Other
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description