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- PDB-6vci: Lipophilic envelope-spanning tunnel protein (LetB), domains MCE2-MCE3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vci | ||||||||||||||||||
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Title | Lipophilic envelope-spanning tunnel protein (LetB), domains MCE2-MCE3 | ||||||||||||||||||
![]() | Lipophilic envelope-spanning tunnel protein LetB | ||||||||||||||||||
![]() | LIPID TRANSPORT / bacterial cell envelope / MCE / YebT / LetB | ||||||||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||||||||
![]() | 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.7 KB | Display | ![]() |
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PDB format | ![]() | 141.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 250.3 KB | Display | ![]() |
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Full document | ![]() | 250.2 KB | Display | |
Data in XML | ![]() | 937 B | Display | |
Data in CIF | ![]() | 5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v0cC ![]() 6v0dC ![]() 6v0eC ![]() 6v0fSC ![]() 6v0gC ![]() 6v0hC ![]() 6v0iC ![]() 6v0jC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25419.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: yebT, b1834, JW1823 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Crystals grew from drops consisting of 100 nL protein plus 100 nL of a reservoir solution consisting of 0.1 M Tris pH 8.5, 20% w/v PEG 1K, and were cryoprotected by supplementing the ...Details: Crystals grew from drops consisting of 100 nL protein plus 100 nL of a reservoir solution consisting of 0.1 M Tris pH 8.5, 20% w/v PEG 1K, and were cryoprotected by supplementing the reservoir solution with 15% ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.32 Å / Num. obs: 27654 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.15→2.21 Å / Num. unique obs: 26145 / CC1/2: 0.62 / Rrim(I) all: 1.26 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6V0F Resolution: 2.15→41 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.15→41 Å
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LS refinement shell | Resolution: 2.1502→2.2362 Å
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