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- PDB-8byt: Outer membrane attachment porin OmpM1 from Veillonella parvula, C... -

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Basic information

Entry
Database: PDB / ID: 8byt
TitleOuter membrane attachment porin OmpM1 from Veillonella parvula, C3 symmetry
ComponentsS-layer homology domain-containing protein
KeywordsMEMBRANE PROTEIN / Porin / outer membrane / attachment / peptidoglycan-binding
Function / homologyS-layer / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / S-layer homology domain-containing protein
Function and homology information
Biological speciesVeillonella parvula (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsSilale, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes.
Authors: Augustinas Silale / Yiling Zhu / Jerzy Witwinowski / Robert E Smith / Kahlan E Newman / Satya P Bhamidimarri / Arnaud Baslé / Syma Khalid / Christophe Beloin / Simonetta Gribaldo / Bert van den Berg /
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 ...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.
History
DepositionDec 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer homology domain-containing protein
B: S-layer homology domain-containing protein
C: S-layer homology domain-containing protein


Theoretical massNumber of molelcules
Total (without water)142,6653
Polymers142,6653
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 113 - 420 / Label seq-ID: 128 - 435

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2AA
d_3CC

NCS oper:
IDCodeMatrixVector
1given(-0.500617523885, 0.865668340376, 0.000647494844289), (-0.865668508575, -0.500617650256, 3.89071434873E-5), (0.000357828029832, -0.000541038298332, 0.999999789618)109.19824583, 407.440580381, 0.0202750881794
2given(-0.499934973482, -0.866062886218, 0.000315286131349), (0.866062854088, -0.499935054201, -0.00027267125654), (0.000393773044592, 0.000136739709363, 0.999999913123)407.338655593, 109.215514579, -0.094569540053

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Components

#1: Protein S-layer homology domain-containing protein


Mass: 47555.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: SKV38 / Gene: D3219_09385 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A0A100YN03

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Veillonella parvula OmpM1 outer membrane attachment porin with enforced C3 symmetry
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.130 MDa / Experimental value: NO
Source (natural)Organism: Veillonella parvula (bacteria) / Strain: SKV38
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Details: 10 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 0.12% decyl maltoside (DM)
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 240000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4284

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
2EPUimage acquisition
4cryoSPARC3.3.2CTF correction
7Buccaneermodel fitting
9cryoSPARC3.3.2initial Euler assignment
10cryoSPARC3.3.2final Euler assignment
12cryoSPARC3.3.23D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119001 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 60.35 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00137212
ELECTRON MICROSCOPYf_angle_d0.35569723
ELECTRON MICROSCOPYf_chiral_restr0.0405981
ELECTRON MICROSCOPYf_plane_restr0.00151305
ELECTRON MICROSCOPYf_dihedral_angle_d3.64481014
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BELECTRON MICROSCOPYNCS constraints3.90329123835E-12
ens_1d_3BELECTRON MICROSCOPYNCS constraints1.16547115584E-10

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