3RGD

Iron loaded frog M ferritin. Short soaking time


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the ferroxidase site of ferritins from higher eukaryotes.

Bertini, I.Lalli, D.Mangani, S.Pozzi, C.Rosa, C.Theil, E.C.Turano, P.

(2012) J Am Chem Soc 134: 6169-6176

  • DOI: https://doi.org/10.1021/ja210084n
  • Primary Citation of Related Structures:  
    3RBC, 3RE7, 3RGD, 4DAS

  • PubMed Abstract: 

    The first step of iron biomineralization mediated by ferritin is the oxidation at the ferroxidase active site of two ferrous ions to a diferric oxo/hydroxo species. Metal-loaded ferritin crystals obtained by soaking crystals of frog ferritin in FeSO(4) and CuSO(4) solutions followed by flash freezing provided X-ray crystal structures of the tripositive iron and bipositive copper adducts at 2.7 and 2.8 Å resolution, respectively. At variance with the already available structures, the crystal form used in this study contains 24 independent subunits in the asymmetric unit permitting comparison between them. For the first time, the diferric species at the ferroxidase site is identified in ferritins from higher eukaryotes. Anomalous difference Fourier maps for crystals (iron crystal 1) obtained after long soaking times in FeSO(4) solution invariantly showed diferric species with a Fe-Fe average distance of 3.1 ± 0.1 Å, strongly indicative of the presence of a μ-oxo/hydroxo bridge between the irons; protein ligands for each iron ion (Fe1 and Fe2) were also unequivocally identified and found to be the same in all subunits. For copper bound ferritin, dicopper(II) centers are also observed. While copper at site 1 is essentially in the same position and has the same coordination environment as Fe1, copper at site 2 is displaced toward His54, now acting as a ligand; this results in an increased intermetal distance (4.3 ± 0.4 Å). His54 coordination and longer metal-metal distances might represent peculiar features of divalent cations at the ferroxidase site. This oxidation-dependent structural information may provide key features for the mechanistic pathway in ferritins from higher eukaryotes that drive uptake of bivalent cation and release of ferric products at the catalytic site. This mechanism is supported by the X-ray picture obtained after only 1 min of soaking in FeSO(4) solutions (iron crystal 2) which reasonably contain the metal at different oxidation states. Here two different di-iron species are trapped in the active site, with intermetal distances corresponding to those of the ferric dimer in crystal 1 and of the dicopper centers and corresponding rearrangement of the His54 side chain.


  • Organizational Affiliation

    Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Florence, Italy. ivanobertini@cerm.unifi.it


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin, middle subunit
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
176Aquarana catesbeianaMutation(s): 0 
EC: 1.16.3.1
UniProt
Find proteins for P07798 (Aquarana catesbeiana)
Explore P07798 
Go to UniProtKB:  P07798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07798
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth J]
AC [auth U]
BA [auth B]
BB [auth J]
AA [auth B],
AB [auth J],
AC [auth U],
BA [auth B],
BB [auth J],
BC [auth U],
CA [auth B],
CB [auth K],
CC [auth V],
DA [auth C],
DB [auth K],
DC [auth V],
EA [auth C],
EB [auth K],
EC [auth W],
FA [auth C],
FB [auth L],
FC [auth W],
GA [auth C],
GB [auth L],
GC [auth X],
HA [auth D],
HB [auth M],
HC [auth X],
IA [auth D],
IB [auth M],
JA [auth D],
JB [auth N],
KA [auth D],
KB [auth N],
LA [auth E],
LB [auth N],
MA [auth E],
MB [auth O],
NA [auth E],
NB [auth O],
OA [auth F],
OB [auth O],
PA [auth F],
PB [auth P],
QA [auth F],
QB [auth P],
RA [auth G],
RB [auth Q],
SA [auth G],
SB [auth Q],
TA [auth H],
TB [auth R],
UA [auth H],
UB [auth R],
VA [auth H],
VB [auth S],
WA [auth I],
WB [auth S],
XA [auth I],
XB [auth T],
Y [auth A],
YA [auth I],
YB [auth T],
Z [auth A],
ZA [auth J],
ZB [auth T]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.744α = 90
b = 210.744β = 90
c = 322.036γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description