9HPN | pdb_00009hpn

Corynebacterium glutamicum PS2 S-layer

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Corynebacterium glutamicum
  • Mutation(s): No 

  • Deposited: 2024-12-13 Released: 2025-01-29 
  • Deposition Author(s): Isbilir, B., Bharat, T.
  • Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust, Human Frontier Science Program (HFSP), European Molecular Biology Organization (EMBO), Leverhulme Trust, The Lister Institute of Preventive Medicine

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mapping the ultrastructural topology of the corynebacterial cell surface.

Isbilir, B.Yeates, A.Alva, V.Bharat, T.A.M.

(2025) PLoS Biol 23: e3003130-e3003130

  • DOI: https://doi.org/10.1371/journal.pbio.3003130
  • Primary Citation of Related Structures:  
    9HPN

  • PubMed Abstract: 

    Corynebacterium glutamicum is a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial family Mycobacteriaceae, which is characterized by a highly unusual cell envelope with an outer membrane consisting of mycolic acids, called mycomembrane. The mycomembrane is further coated by a surface (S-)layer array in C. glutamicum, making this cell envelope highly distinctive. Despite the biotechnological significance of C. glutamicum and biomedical significance of mycomembrane-containing pathogens, ultrastructural and molecular details of its distinctive cell envelope remain poorly characterized. To address this, we investigated the cell envelope of C. glutamicum using electron cryotomography and cryomicroscopy of focused ion beam-milled single and dividing cells. Our cellular imaging allowed us to map the different components of the cell envelope onto the tomographic density. Our data reveal that C. glutamicum has a variable cell envelope, with the S-layer decorating the mycomembrane in a patchy manner. We further isolated and resolved the structure of the S-layer at 3.1 Å-resolution using single particle electron cryomicroscopy. Our structure shows that the S-layer of C. glutamicum is composed of a hexagonal array of the PS2 protein, which interacts directly with the mycomembrane via an anchoring segment containing a coiled-coil motif. Bioinformatic analyses revealed that the PS2 S-layer is sparsely yet exclusively present within the Corynebacterium genus and absent in other genera of the Mycobacteriaceae family, suggesting distinct evolutionary pathways in the development of their cell envelopes. Our structural and cellular data collectively provide a topography of the unusual C. glutamicum cell surface, features of which are shared by many pathogenic and microbiome-associated bacteria, as well as by several industrially significant bacterial species.


  • Organizational Affiliation

    Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PS2
A, B, C, D, E
A, B, C, D, E, F
498Corynebacterium glutamicumMutation(s): 0 
UniProt
Find proteins for Q6QUU5 (Corynebacterium glutamicum)
Explore Q6QUU5 
Go to UniProtKB:  Q6QUU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6QUU5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.5.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/31
Wellcome TrustUnited Kingdom225317/Z/22/Z
Human Frontier Science Program (HFSP)FranceRGY0074/2021
European Molecular Biology Organization (EMBO)European UnionYIP 2021
Leverhulme TrustUnited KingdomPhilip Leverhulme Prize
The Lister Institute of Preventive MedicineUnited KingdomLister Prize

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references