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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Outer membrane attachment porin OmpM1 from Veillonella parvula | |||||||||
![]() | B-factor (-70.2 angstrom sq.) sharpened map from non-uniform refinement | |||||||||
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![]() | Porin / outer membrane / attachment / peptidoglycan-binding / 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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
![]() | Silale A / van den Berg B | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 778.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.9 KB | Display | ![]() |
Images | ![]() | 40.8 KB | ||
Masks | ![]() | 824 MB | ![]() | |
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 765.5 MB 765.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bymMC ![]() 8bysC ![]() 8bytC ![]() 8bz2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | B-factor (-70.2 angstrom sq.) sharpened map from non-uniform refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.574 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: Half map B
File | emd_16328_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_16328_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Veillonella parvula OmpM1 outer membrane attachment porin trimer
Entire | Name: Veillonella parvula OmpM1 outer membrane attachment porin trimer |
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Components |
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-Supramolecule #1: Veillonella parvula OmpM1 outer membrane attachment porin trimer
Supramolecule | Name: Veillonella parvula OmpM1 outer membrane attachment porin trimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: S-layer homology domain-containing protein
Macromolecule | Name: S-layer homology domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 47.555062 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 11.6 mg/mL |
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Buffer | pH: 7.5 Details: 10 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 0.12% decyl maltoside (DM) |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4284 / Average electron dose: 50.1 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 240000 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8bym: |