4PT2

Myxococcus xanthus encapsulin protein (EncA)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress.

McHugh, C.A.Fontana, J.Nemecek, D.Cheng, N.Aksyuk, A.A.Heymann, J.B.Winkler, D.C.Lam, A.S.Wall, J.S.Steven, A.C.Hoiczyk, E.

(2014) Embo J. 33: 1896-1911

  • DOI: 10.15252/embj.201488566

  • PubMed Abstract: 
  • Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of ...

    Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration.


    Organizational Affiliation

    W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA stevena@mail.nih.gov ehoiczyk@jhsph.edu.,W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA stevena@mail.nih.gov ehoiczyk@jhsph.edu.,Department of Biology, Brookhaven National Laboratory, Upton, NY, USA.,Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Encapsulin protein
P, A, B
287Myxococcus xanthus (strain DK 1622)Mutation(s): 0 
Find proteins for Q1D6H4 (Myxococcus xanthus (strain DK 1622))
Go to UniProtKB:  Q1D6H4
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection
  • Version 1.3: 2019-05-08
    Type: Data collection, Structure summary