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Yorodumi- EMDB-48835: Cryo-EM structure of an extended F. johnsoniae BAM complex, compo... -
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Open data
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Basic information
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| Title | Cryo-EM structure of an extended F. johnsoniae BAM complex, composite map | |||||||||
Map data | composite map | |||||||||
Sample |
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Keywords | BAM complex / BamA / BamD / BamG / BamH / BamM / BamP / outer-membrane proteins / OMP / MEMBRANE PROTEIN | |||||||||
| Function / homology | Function and homology informationmembrane assembly / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / calcium ion binding Similarity search - Function | |||||||||
| Biological species | Flavobacterium johnsoniae UW101 (bacteria) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Deme JC / Lea SM | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2025Title: A shared mechanism for Bacteroidota protein transport and gliding motility. Authors: Xiaolong Liu / Marieta Avramova / Justin C Deme / Rachel L Jones / Camilla A K Lundgren / Susan M Lea / Ben C Berks / ![]() Abstract: Bacteria of the phylum Bacteroidota are major human commensals and pathogens in addition to being abundant members of the wider biosphere. Bacteroidota move by gliding and they export proteins using ...Bacteria of the phylum Bacteroidota are major human commensals and pathogens in addition to being abundant members of the wider biosphere. Bacteroidota move by gliding and they export proteins using the Type 9 Secretion System (T9SS). Here we discover that gliding motility and the T9SS share an unprecedented mechanism of energisation in which outer membrane proteins are covalently attached by disulfide bonds to a moving internal track structure that propels them laterally through the membrane. We determined the structure of an exemplar Bacteroidota mobile track by obtaining the cryoEM structure of a 3 MDa circular mini-track from Porphyromonas gingivalis. Our discoveries identify a mechanistic and evolutionary link between gliding motility and T9SS-dependent protein transport. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_48835.map.gz | 252.9 MB | EMDB map data format | |
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| Header (meta data) | emd-48835-v30.xml emd-48835.xml | 26 KB 26 KB | Display Display | EMDB header |
| Images | emd_48835.png | 141.1 KB | ||
| Filedesc metadata | emd-48835.cif.gz | 8.5 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-48835 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-48835 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9n2dMC ![]() 9n2eC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_48835.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | composite map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.732 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : BAM complex
+Supramolecule #1: BAM complex
+Macromolecule #1: Bam D
+Macromolecule #2: Bam A
+Macromolecule #3: Bam H
+Macromolecule #4: Bam G
+Macromolecule #5: Bam M
+Macromolecule #6: Bam P
+Macromolecule #9: DIACYL GLYCEROL
+Macromolecule #10: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(...
+Macromolecule #11: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #12: alpha-D-mannopyranose
+Macromolecule #13: PALMITIC ACID
+Macromolecule #14: CALCIUM ION
+Macromolecule #15: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 8 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.3 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Flavobacterium johnsoniae UW101 (bacteria)
Authors
United States, 1 items
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Processing
FIELD EMISSION GUN
