+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0788 | |||||||||
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Title | Domain 5-7 of YebT in conformation 2 | |||||||||
Map data | domain 5-7 of YebT in conformation 2 | |||||||||
Sample |
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Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||
Authors | Liu C / Zhang L / Wang HW / Wang J / Li XM | |||||||||
Funding support | China, 2 items
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Citation | Journal: J Mol Biol / Year: 2020 Title: Cryo-EM Structure of a Bacterial Lipid Transporter YebT. Authors: Chuan Liu / Jinying Ma / Jia Wang / Hongwei Wang / Li Zhang / Abstract: The outer membrane (OM) of Gram-negative bacteria is asymmetric, with lipopolysaccharides (LPSs) on the outer surface and phospholipids (PLs) on the inner surface. This unique organization of OM ...The outer membrane (OM) of Gram-negative bacteria is asymmetric, with lipopolysaccharides (LPSs) on the outer surface and phospholipids (PLs) on the inner surface. This unique organization of OM makes Gram-negative bacteria resistant to many toxic chemicals. How this asymmetric distribution of lipids is maintained has been studied for decades with previous reports of an Mla (Maintenance of OM Lipid Asymmetry) system to be involved. Furthermore, the OM of Gram-negative bacteria is about 20 nm away from inner membrane (IM) where the lipids are synthesized. Therefore, how nascent lipids travel across the periplasmic space and arrive at the inner surface of OM is another interesting question. YebT is a homologue of MlaD in the Mla pathway, but its role in lipid distribution of the OM and IM is largely unknown. Here we report the first high-resolution (~3.0 Å) cryo-EM structure of full-length E. coli YebT in a substrate-bound state. Our structure with details of lipid interaction indicates that YebT is a lipid transporter spanning between IM and OM. We also demonstrate the symmetry mismatch in YebT and the existence of many other conformations of YebT revealing the intrinsic dynamics of this lipid channel. And a brief discussion on possible mechanisms of lipid transport is also included. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0788.map.gz | 10.6 MB | EMDB map data format | |
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Header (meta data) | emd-0788-v30.xml emd-0788.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | emd_0788.png | 29.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0788 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0788 | HTTPS FTP |
-Related structure data
Related structure data | 0784C 0785C 0786C 0787C 6kz3C 6kz4C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0788.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | domain 5-7 of YebT in conformation 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : YT-C
Entire | Name: YT-C |
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Components |
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-Supramolecule #1: YT-C
Supramolecule | Name: YT-C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: C-terminal part of YebT |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 570 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: OTHER / Number images used: 57300 |