1LB3

Structure of recombinant mouse L chain ferritin at 1.2 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural description of the active sites of mouse L-chain ferritin at 1.2A resolution

Granier, T.Langlois D'Estaintot, B.Gallois, B.Chevalier, J.-M.Precigoux, G.Santambrogio, P.Arosio, P.

(2003) J.Biol.Inorg.Chem. 8: 105-111

  • DOI: 10.1007/s00775-002-0389-4

  • PubMed Abstract: 
  • The first ferritin structure refined at the atomic level has been achieved on recombinant mouse L-chain apoferritin (rMoLF) crystals. These latter diffract to 1.2 A resolution under cryogenic conditions. When cryo-cooling the sample, the thermal diso ...

    The first ferritin structure refined at the atomic level has been achieved on recombinant mouse L-chain apoferritin (rMoLF) crystals. These latter diffract to 1.2 A resolution under cryogenic conditions. When cryo-cooling the sample, the thermal disorder usually observed at room temperature is reduced and the low-temperature structure reveals several details concerning the protein putative active sites and their properties. Within the pores built up by the molecular three-fold symmetry axes, the iron entry route to the ferritin cavity, residues H118, D131 and E134, exhibit alternate conformations associated with the binding of partially hydrated cadmium ions, a metal used as a crystallization agent. At the mineral ferrihydrite nucleation center, the electron density maps evidence the orientation of E57, E60, E61 and E64 glutamate side chains (whereas they were observed highly disordered in previous ferritin structures determined at room temperature) and allow a description of the site taking into account the binding geometry of four Cd(2+) ions. Moreover, the side chain of residue K140, lying in the vicinity of the ferrihydrite nucleation center, is shown to interact with residue E61. As previously highlighted, this observation confirms the importance of K140 in the rMoLF sequence, as being responsible for the low level of iron incorporation by mousel L-chain ferritin compared to human L-chain ferritin. Finally, the diffusion of small molecules within the ferritin cavity is illustrated here by the presence of ordered molecules of glycerol used as a cryo-protectant, which bind the inner cavity surface of the protein.


    Organizational Affiliation

    Unité de Biophysique Structurale, UMR CNRS 5471, Université Bordeaux I, Bât B8, avenue des Facultés, 33405 Talence Cedex, France. t.granier@ubs.u-bordeaux.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERRITIN LIGHT CHAIN 1
A
182Mus musculusGene Names: Ftl1 (Ftl, Ftl-1)
Find proteins for P29391 (Mus musculus)
Go to UniProtKB:  P29391
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: 1.21 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.132 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 180.590α = 90.00
b = 180.590β = 90.00
c = 180.590γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97model building
SCALAdata scaling
MOSFLMdata reduction
SHELXL-97refinement
SHELXL-97phasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-02-01
    Type: Structure summary