5DJB

Structure of the Haliangium ochraceum BMC-H shell protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy.

Sutter, M.Faulkner, M.Aussignargues, C.Paasch, B.C.Barrett, S.Kerfeld, C.A.Liu, L.N.

(2016) Nano Lett 16: 1590-1595

  • DOI: https://doi.org/10.1021/acs.nanolett.5b04259
  • Primary Citation of Related Structures:  
    5DJB

  • PubMed Abstract: 

    Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla. They compartmentalize enzymes within a selectively permeable shell and play important roles in CO2 fixation, pathogenesis, and microbial ecology. Here, we combine X-ray crystallography and high-speed atomic force microscopy to characterize, at molecular resolution, the structure and dynamics of BMC shell facet assembly. Our results show that preformed hexamers assemble into uniformly oriented shell layers, a single hexamer thick. We also observe the dynamic process of shell facet assembly. Shell hexamers can dissociate from and incorporate into assembled sheets, indicating a flexible intermolecular interaction. Furthermore, we demonstrate that the self-assembly and dynamics of shell proteins are governed by specific contacts at the interfaces of shell proteins. Our study provides novel insights into the formation, interactions, and dynamics of BMC shell facets, which are essential for the design and engineering of self-assembled biological nanoreactors and scaffolds based on BMC architectures.


  • Organizational Affiliation

    MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microcompartments protein
A, B, C, D, E
A, B, C, D, E, F, G, H
99Haliangium ochraceum DSM 14365Mutation(s): 0 
Gene Names: Hoch_5815
UniProt
Find proteins for D0LID5 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2))
Explore D0LID5 
Go to UniProtKB:  D0LID5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0LID5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.176 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.2α = 90
b = 69.2β = 90
c = 120.418γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description