4ML5

one minute iron loaded frog M ferritin mutant H54Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Time-lapse anomalous X-ray diffraction shows how Fe(2+) substrate ions move through ferritin protein nanocages to oxidoreductase sites.

Pozzi, C.Di Pisa, F.Lalli, D.Rosa, C.Theil, E.Turano, P.Mangani, S.

(2015) Acta Crystallogr.,Sect.D 71: 941-953

  • DOI: 10.1107/S1399004715002333
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ferritin superfamily protein cages reversibly synthesize internal biominerals, Fe2O3·H2O. Fe(2+) and O2 (or H2O2) substrates bind at oxidoreductase sites in the cage, initiating biomineral synthesis to concentrate iron and prevent potentially toxic r ...

    Ferritin superfamily protein cages reversibly synthesize internal biominerals, Fe2O3·H2O. Fe(2+) and O2 (or H2O2) substrates bind at oxidoreductase sites in the cage, initiating biomineral synthesis to concentrate iron and prevent potentially toxic reactions products from Fe(2+)and O2 or H2O2 chemistry. By freezing ferritin crystals of Rana catesbeiana ferritin M (RcMf) at different time intervals after exposure to a ferrous salt, a series of high-resolution anomalous X-ray diffraction data sets were obtained that led to crystal structures that allowed the direct observation of ferrous ions entering, moving along and binding at enzyme sites in the protein cages. The ensemble of crystal structures from both aerobic and anaerobic conditions provides snapshots of the iron substrate bound at different cage locations that vary with time. The observed differential occupation of the two iron sites in the enzyme oxidoreductase centre (with Glu23 and Glu58, and with Glu58, His61 and Glu103 as ligands, respectively) and other iron-binding sites (with Glu53, His54, Glu57, Glu136 and Asp140 as ligands) reflects the approach of the Fe(2+) substrate and its progression before the enzymatic cycle 2Fe(2+) + O2 → Fe(3+)-O-O-Fe(3+) → Fe(3+)-O(H)-Fe(3+) and turnover. The crystal structures also revealed different Fe(2+) coordination compounds bound to the ion channels located at the threefold and fourfold symmetry axes of the cage.


    Organizational Affiliation

    Dipartimento di Chimica and CERM, University of Florence, Via Della Lastruccia 3, Sesto Fiorentino, 50019 Firenze, Italy.,Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.,Children's Hospital, Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin, middle subunit
A
176Lithobates catesbeianaMutation(s): 1 
EC: 1.16.3.1
Find proteins for P07798 (Lithobates catesbeiana)
Go to UniProtKB:  P07798
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.139 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 184.230α = 90.00
b = 184.230β = 90.00
c = 184.230γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Non-polymer description
  • Version 1.2: 2015-04-15
    Type: Database references