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- EMDB-16328: Outer membrane attachment porin OmpM1 from Veillonella parvula -

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Basic information

Entry
Database: EMDB / ID: EMD-16328
TitleOuter membrane attachment porin OmpM1 from Veillonella parvula
Map dataB-factor (-70.2 angstrom sq.) sharpened map from non-uniform refinement
Sample
  • Complex: Veillonella parvula OmpM1 outer membrane attachment porin trimer
    • Protein or peptide: S-layer homology domain-containing protein
KeywordsPorin / outer membrane / attachment / peptidoglycan-binding / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsSilale A / van den Berg B
Funding support United Kingdom, 1 items
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, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16328.png

Downloads & links

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Map

FileDownload / File: emd_16328.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor (-70.2 angstrom sq.) sharpened map from non-uniform refinement
Voxel sizeX=Y=Z: 0.574 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.38394442 - 0.622058
Average (Standard dev.)0.00018233774 (±0.008989683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16328_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_16328_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_16328_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Veillonella parvula OmpM1 outer membrane attachment porin trimer

EntireName: Veillonella parvula OmpM1 outer membrane attachment porin trimer
Components
  • Complex: Veillonella parvula OmpM1 outer membrane attachment porin trimer
    • Protein or peptide: S-layer homology domain-containing protein

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Supramolecule #1: Veillonella parvula OmpM1 outer membrane attachment porin trimer

SupramoleculeName: Veillonella parvula OmpM1 outer membrane attachment porin trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Veillonella parvula (bacteria) / Strain: SKV38
Molecular weightTheoretical: 130 KDa

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

MacromoleculeName: S-layer homology domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Veillonella parvula (bacteria) / Strain: SKV38
Molecular weightTheoretical: 47.555062 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRYIRQLCCV SLLCLSGSAA AANVRLQHHH HHHHLEAANP FSDVTPDSWA YQAVSQLAQA GIVNGYPDGT FKGQNNITRY EMAQMVAKA MANQDRANAE QQAMINRLAD EFSNELNNLG VRVSRLEDRV GNVKVTGDAR IRYQGSEDKG VYKANSKSLT D GRARVQFN ...String:
MRYIRQLCCV SLLCLSGSAA AANVRLQHHH HHHHLEAANP FSDVTPDSWA YQAVSQLAQA GIVNGYPDGT FKGQNNITRY EMAQMVAKA MANQDRANAE QQAMINRLAD EFSNELNNLG VRVSRLEDRV GNVKVTGDAR IRYQGSEDKG VYKANSKSLT D GRARVQFN ANVNDKTQAV VRVKGNYEFG DSTKGSQATI DRAYVDHKFG SNVSAKAGRF QQTIGGGLMY DDTFDGAQLN VG NDKVQVQ GAYGYMIDGA ADGNSKSDNP SVSYVGLKGK VGKESSVGGF YSRLSSGNLN HNGVTVNSDK QDVYGFNADF RKN KLWAGG EWLKASNVDN SQAWTAGLGY GNYDIAKKGT WDVKGQYFNQ KANAPIVSST WDQAYDLTNT SNGYKGYMAS VDYA VQDNV GLSAGYGFNS KDQSGNDLSD FYRAELNYKF

UniProtKB: S-layer homology domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration11.6 mg/mL
BufferpH: 7.5
Details: 10 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 0.12% decyl maltoside (DM)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 240000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4284 / Average electron dose: 50.1 e/Å2

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) / Details: Non-uniform refinement
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 96280
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8bym:
Outer membrane attachment porin OmpM1 from Veillonella parvula

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