5DA5

Crystal structure of Rhodospirillum rubrum Rru_A0973


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.064 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments.

He, D.Hughes, S.Vanden-Hehir, S.Georgiev, A.Altenbach, K.Tarrant, E.J.Mackay, C.L.Waldron, K.J.Clarke, D.J.Marles-Wright, J.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.18972
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ferritins are ubiquitous proteins that oxidise and store iron within a protein shell to protect cells from oxidative damage. We have characterized the structure and function of a new member of the ferritin superfamily that is sequestered within an en ...

    Ferritins are ubiquitous proteins that oxidise and store iron within a protein shell to protect cells from oxidative damage. We have characterized the structure and function of a new member of the ferritin superfamily that is sequestered within an encapsulin capsid. We show that this encapsulated ferritin (EncFtn) has two main alpha helices, which assemble in a metal dependent manner to form a ferroxidase center at a dimer interface. EncFtn adopts an open decameric structure that is topologically distinct from other ferritins. While EncFtn acts as a ferroxidase, it cannot mineralize iron. Conversely, the encapsulin shell associates with iron, but is not enzymatically active, and we demonstrate that EncFtn must be housed within the encapsulin for iron storage. This encapsulin nanocompartment is widely distributed in bacteria and archaea and represents a distinct class of iron storage system, where the oxidation and mineralization of iron are distributed between two proteins.


    Organizational Affiliation

    Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rru_A0973
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d
116Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1)Mutation(s): 0 
Find proteins for Q2RVS1 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1))
Go to UniProtKB:  Q2RVS1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOA
Query on GOA

Download SDF File 
Download CCD File 
a, A, B, C, D, F, G, K, L, N, P, Q, U, V, X, Z
GLYCOLIC ACID
HYDROXYACETIC ACID; HYDROXYETHANOIC ACID
C2 H4 O3
AEMRFAOFKBGASW-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, a, B, c, C, D, F, G, I, J, K, L, N, P, Q, U, V, X, Z
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, a, B, D, F, G, K, L, N, P, Q, U, V, X, Z
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.064 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 98.184α = 90.00
b = 120.533β = 95.36
c = 140.250γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China Scholarships CouncilChina--
Royal SocietyUnited KingdomRG130585

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-31
    Type: Database references
  • Version 1.2: 2018-01-31
    Type: Author supporting evidence