6XPL

CutR Screw, form 2 with 33.8 angstrom pitch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.219 

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

Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization.

Ochoa, J.M.Nguyen, V.N.Nie, M.Sawaya, M.R.Bobik, T.A.Yeates, T.O.

(2020) Protein Sci 29: 2201-2212

  • DOI: https://doi.org/10.1002/pro.3941
  • Primary Citation of Related Structures:  
    6XPH, 6XPI, 6XPJ, 6XPK, 6XPL

  • PubMed Abstract: 

    Bacterial microcompartments are protein-based organelles that carry out specialized metabolic functions in diverse bacteria. Their outer shells are built from several thousand protein subunits. Some of the architectural principles of bacterial microcompartments have been articulated, with lateral packing of flat hexameric BMC proteins providing the basic foundation for assembly. Nonetheless, a complete understanding has been elusive, partly owing to polymorphic mechanisms of assembly exhibited by most microcompartment types. An earlier study of one homologous BMC shell protein subfamily, EutS/PduU, revealed a profoundly bent, rather than flat, hexameric structure. The possibility of a specialized architectural role was hypothesized, but artifactual effects of crystallization could not be ruled out. Here we report a series of crystal structures of an orthologous protein, CutR, from a glycyl-radical type choline-utilizing microcompartment from the bacterium Streptococcus intermedius. Depending on crystal form, expression construct, and minor mutations, a range of novel quaternary architectures was observed, including two spiral hexagonal assemblies. A new graphical approach helps illuminate the variations in BMC hexameric structure, with results substantiating the idea that the EutS/PduU/CutR subfamily of BMC proteins may endow microcompartment shells with flexible modes of assembly.


  • Organizational Affiliation

    UCLA-Molecular Biology Institute, University of California, Los Angeles (UCLA), California, Los Angeles, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ethanolamine utilization protein EutS123Streptococcus intermedius SK54 = ATCC 27335Mutation(s): 0 
Gene Names: HMPREF1654_00416
UniProt
Find proteins for A0A0E2IV13 (Streptococcus intermedius (strain ATCC 27335 / DSM 20573 / CCUG 32759 / CIP 103248 / JCM 12996 / LMG 17840 / NCTC 11324 / SK54 / 1877))
Explore A0A0E2IV13 
Go to UniProtKB:  A0A0E2IV13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E2IV13
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.219 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.91α = 90
b = 64.91β = 90
c = 33.78γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-11-11
    Changes: Database references
  • Version 1.3: 2021-06-30
    Changes: Data collection
  • Version 1.4: 2023-10-18
    Changes: Data collection, Database references, Refinement description