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- EMDB-16332: Outer membrane attachment porin OmpM1 from Veillonella parvula, native -

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Basic information

Entry
Database: EMDB / ID: EMD-16332
TitleOuter membrane attachment porin OmpM1 from Veillonella parvula, native
Map dataB-factor sharpened (-97.5 angstrom sq.) map from non-uniform refinement
Sample
  • Complex: Outer membrane attachment porin OmpM1 trimer
    • Protein or peptide: S-layer homology domain-containing protein
KeywordsOuter membrane attachment / porin / peptidoglycan-binding / nutrient transport / MEMBRANE PROTEIN
Function / homology: / S-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: 3.28 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_16332.png

Downloads & links

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Map

FileDownload / File: emd_16332.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened (-97.5 angstrom sq.) map from non-uniform refinement
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 300 pix.
= 344.4 Å		1.15 Å/pix.
x 300 pix.
= 344.4 Å		1.15 Å/pix.
x 300 pix.
= 344.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.148 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.241
Minimum - Maximum-1.4783549 - 1.960775
Average (Standard dev.)-0.00019185434 (±0.028547015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16332_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: Half map 1

Fileemd_16332_half_map_1.map
AnnotationHalf map 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_16332_half_map_2.map
AnnotationHalf map 2
Projections & Slices
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Sample components

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Entire : Outer membrane attachment porin OmpM1 trimer

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

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Supramolecule #1: Outer membrane attachment porin OmpM1 trimer

SupramoleculeName: Outer membrane attachment porin OmpM1 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: 46.547863 KDa
Recombinant expressionOrganism: Veillonella parvula (bacteria)
SequenceString: MKKQFATMLA ATAVLGVTTA FAANPFSDVT PDSWAYQAVS QLAQAGIVNG YPDGTFKGQN NITRYEMAQM VAKAMANQDR ANAEQQAMI NRLADEFSNE LNNLGVRVSR LEDRVGNVKV TGDARIRYQG SEDKGVYKAN SKSLTDGRAR VQFNANVNDK T QAVVRVKG ...String:
MKKQFATMLA ATAVLGVTTA FAANPFSDVT PDSWAYQAVS QLAQAGIVNG YPDGTFKGQN NITRYEMAQM VAKAMANQDR ANAEQQAMI NRLADEFSNE LNNLGVRVSR LEDRVGNVKV TGDARIRYQG SEDKGVYKAN SKSLTDGRAR VQFNANVNDK T QAVVRVKG NYEFGDSTKG SQATIDRAYV DHKFGSNVSA KAGRFQQTIG GGLMYDDTFD GAQLNVGNDK VQVQGAYGYM ID GAADGNS KSDNPSVSYV GLKGKVGKES SVGGFYSRLS SGNLNHNGVT VNSDKQDVYG FNADFRKNKL WAGGEWLKAS NVD NSQAWT AGLGYGNYDI AKKGTWDVKG QYFNQKANAP IVSSTWDQAY DLTNTSNGYK GYMASVDYAV QDNVGLSAGY GFNS KDQSG NDLSDFYRAE LNYKFGGHHH HHH

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

Concentration8 mg/mL
BufferpH: 7.5
Details: 10 mM HEPES-NaOH, 100 mM NaCl, 0.12% decyl maltoside
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

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 6505 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 240000

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 144245
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8bys:
Outer membrane attachment porin OmpM1 from Veillonella parvula, native

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