8BYT | pdb_00008byt

Outer membrane attachment porin OmpM1 from Veillonella parvula, C3 symmetry

• PDB DOI: https://doi.org/10.2210/pdb8BYT/pdb
• EM Map EMD-16333: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Veillonella parvula
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2022-12-13 Released: 2023-11-08 
• Deposition Author(s): Silale, A., van den Berg, B.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8BYM

Literature

Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes.

Silale, A., Zhu, Y., Witwinowski, J., Smith, R.E., Newman, K.E., Bhamidimarri, S.P., Basle, A., Khalid, S., Beloin, C., Gribaldo, S., van den Berg, B.

(2023) Nat Commun 14: 7152-7152

• PubMed: 37932269 
• DOI: https://doi.org/10.1038/s41467-023-42601-y
• Primary Citation Related Structures: 
  8BYM, 8BYS, 8BYT, 8BZ2


• PubMed Abstract: 
  

  The outer membrane (OM) in diderm, or Gram-negative, bacteria must be tethered to peptidoglycan for mechanical stability and to maintain cell morphology. Most diderm phyla from the Terrabacteria group have recently been shown to lack well-characterised OM attachment systems, but instead have OmpM, which could represent an ancestral tethering system in bacteria. Here, we have determined the structure of the most abundant OmpM protein from Veillonella parvula (diderm Firmicutes) by single particle cryogenic electron microscopy. We also characterised the channel properties of the transmembrane β-barrel of OmpM and investigated the structure and PG-binding properties of its periplasmic stalk region. Our results show that OM tethering and nutrient acquisition are genetically linked in V. parvula, and probably other diderm Terrabacteria. This dual function of OmpM may have played a role in the loss of the OM in ancestral bacteria and the emergence of monoderm bacterial lineages.

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Organizational Affiliation: 
• Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK.
Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
Institut Pasteur, Université de Paris Cité, Genetics of Biofilms Laboratory, Paris, France. [e-mail].
Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France. [e-mail].
Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content 

• Total Structure Weight: 142.67 kDa 
• Atom Count: 7,077 
• Modeled Residue Count: 924 
• Deposited Residue Count: 1,305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-layer homology domain-containing protein	A, B, C	435	Veillonella parvula	Mutation(s): 0  Gene Names: D3219_09385 Membrane Entity: Yes
UniProt
Find proteins for A0A100YN03 (Veillonella parvula) Explore A0A100YN03  Go to UniProtKB:  A0A100YN03

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	PHENIX	1.20.1-4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Silale, A., van den Berg, B.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	214222/Z/18/Z

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Database references