1TJO

Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

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This is version 1.3 of the entry. See complete history. 


Literature

Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states.

Zeth, K., Offermann, S., Essen, L.O., Oesterhelt, D.

(2004) Proc Natl Acad Sci U S A 101: 13780-13785

  • DOI: 10.1073/pnas.0401821101
  • Primary Citation of Related Structures:  
    1MOJ, 1TJO, 1TK6, 1TKO, 1TKP

  • PubMed Abstract: 

    • The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents ...

    The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.

    Organizational Affiliation: 

    Department of Membrane Biochemistry, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-rich dpsA-homolog proteinA, B, C, D182Halobacterium salinarumMutation(s): 0 
EC: 1.16
UniProt
Find proteins for Q9HMP7 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore Q9HMP7 
Go to UniProtKB:  Q9HMP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HMP7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
FE
Query on FE
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
K [auth B],
M [auth C],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
M [auth C],
P [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
N [auth C],
Q [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
O [auth C],
R [auth D]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.11α = 90
b = 91.11β = 90
c = 150.04γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
ProDCdata collection
XDSdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description