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Open data
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Basic information
Entry | Database: PDB / ID: 6v0i | ||||||||||||||||||
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Title | Lipophilic Envelope-spanning Tunnel B (LetB), Model 7 | ||||||||||||||||||
![]() | Intermembrane transport protein YebT | ||||||||||||||||||
![]() | LIPID TRANSPORT / conformational dynamics / bacterial cell envelope / LetB / YebT / MCE | ||||||||||||||||||
Function / homology | : / Mce/MlaD / MlaD protein / intermembrane lipid transfer / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane / Intermembrane transport protein YebT![]() | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å | ||||||||||||||||||
![]() | Isom, G.L. / Coudray, N. / MacRae, M.R. / McManus, C.T. / Ekiert, D.C. / Bhabha, G. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: LetB Structure Reveals a Tunnel for Lipid Transport across the Bacterial Envelope. Authors: Georgia L Isom / Nicolas Coudray / Mark R MacRae / Collin T McManus / Damian C Ekiert / Gira Bhabha / ![]() Abstract: Gram-negative bacteria are surrounded by an outer membrane composed of phospholipids and lipopolysaccharide, which acts as a barrier and contributes to antibiotic resistance. The systems that mediate ...Gram-negative bacteria are surrounded by an outer membrane composed of phospholipids and lipopolysaccharide, which acts as a barrier and contributes to antibiotic resistance. The systems that mediate phospholipid trafficking across the periplasm, such as MCE (Mammalian Cell Entry) transporters, have not been well characterized. Our ~3.5 Å cryo-EM structure of the E. coli MCE protein LetB reveals an ~0.6 megadalton complex that consists of seven stacked rings, with a central hydrophobic tunnel sufficiently long to span the periplasm. Lipids bind inside the tunnel, suggesting that it functions as a pathway for lipid transport. Cryo-EM structures in the open and closed states reveal a dynamic tunnel lining, with implications for gating or substrate translocation. Our results support a model in which LetB establishes a physical link between the two membranes and creates a hydrophobic pathway for the translocation of lipids across the periplasm. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 385.1 KB | Display | ![]() |
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PDB format | ![]() | 297.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 20999MC ![]() 6v0cC ![]() 6v0dC ![]() 6v0eC ![]() 6v0fC ![]() 6v0gC ![]() 6v0hC ![]() 6v0jC ![]() 6vciC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Aligned, dose-weighted and non-dose-weighted micrographs [micrographs - single frame] Data #2: Particle stacks for Model 1 (EMD-20993) [picked particles - single frame - processed] Data #3: Particle stacks for Model 2 (EMD-20994) [picked particles - single frame - processed] Data #4: Particle stacks for Model 3 (EMD-20995) [picked particles - single frame - processed] Data #5: Particle stacks for Model 4 (EMD-20996) [picked particles - single frame - processed] Data #6: Particle stacks for Model 5 (EMD-20997) [picked particles - single frame - processed] Data #7: Particle stacks for Model 6 (EMD-20998) [picked particles - single frame - processed] Data #8: Particle stacks for Model 7 (EMD-20999) [picked particles - single frame - processed] Data #9: Particle stacks for Model 8 (EMD-21000) [picked particles - single frame - processed]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 89744.031 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: yebT, b1834, JW1823 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Lipophilic Envelope-spanning Tunnel B (LetB), Map 7, Model 7 Type: COMPLEX Details: Cryo-EM reconstruction of rings 2 to 4, class 1.2.2 Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.56 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4906 |
Image scans | Movie frames/image: 50 / Used frames/image: 1-50 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 731231 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59687 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5UW2 Pdb chain-ID: A / Accession code: 5UW2 / Source name: PDB / Type: experimental model |