6MZX

Cryo-EM structure of the HO BMC shell: Icosahedral reconstruction (main population)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Plasticity of Molecular Interactions Governs Bacterial Microcompartment Shell Assembly.

Greber, B.J.Sutter, M.Kerfeld, C.A.

(2019) Structure 27: 749-763.e4

  • DOI: https://doi.org/10.1016/j.str.2019.01.017
  • Primary Citation of Related Structures:  
    6MZU, 6MZV, 6MZX, 6MZY, 6N06, 6N07, 6N09, 6N0F, 6N0G

  • PubMed Abstract: 

    Bacterial microcompartments (BMCs) are composed of an enzymatic core encapsulated by a selectively permeable protein shell that enhances catalytic efficiency. Many pathogenic bacteria derive competitive advantages from their BMC-based catabolism, implicating BMCs as drug targets. BMC shells are of interest for bioengineering due to their diverse and selective permeability properties and because they self-assemble. A complete understanding of shell composition and organization is a prerequisite for biotechnological applications. Here, we report the cryoelectron microscopy structure of a BMC shell at 3.0-Å resolution, using an image-processing strategy that allowed us to determine the previously uncharacterized structural details of the interactions formed by the BMC-T S and BMC-T D shell subunits in the context of the assembled shell. We found unexpected structural plasticity among these interactions, resulting in distinct shell populations assembled from varying numbers of the BMC-T S and BMC-T D subunits. We discuss the implications of these findings on shell assembly and function.


  • Organizational Affiliation

    California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ethanolamine utilization protein EutN/carboxysome structural protein CcmlA [auth A1]96Haliangium ochraceum DSM 14365Mutation(s): 0 
Gene Names: Hoch_5814
UniProt
Find proteins for D0LHE5 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2))
Explore D0LHE5 
Go to UniProtKB:  D0LHE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0LHE5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Microcompartments protein HO-581599Haliangium 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Microcompartments protein HO-5816H [auth A8],
I [auth A9]
212Haliangium ochraceum DSM 14365Mutation(s): 0 
Gene Names: Hoch_5816
UniProt
Find proteins for D0LID6 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2))
Explore D0LID6 
Go to UniProtKB:  D0LID6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0LID6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONFREALIGN9

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5 R01 AI114975-05
Department of Energy (DOE, United States)United StatesDE-FG01-91ER20021

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description