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Open data
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Basic information
Entry | Database: PDB / ID: 6mhz | ||||||
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Title | Vanadate trapped Cryo-EM Structure of E.coli LptB2FG Transporter | ||||||
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![]() | TRANSPORT PROTEIN/Hydrolase / ABC transporter / lipopolysaccharide / LPS / nanodisc / TRANSPORT PROTEIN-Hydrolase complex | ||||||
Function / homology | ![]() Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
![]() | Orlando, B.J. / Li, Y. / Liao, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of lipopolysaccharide extraction by the LptBFGC complex. Authors: Yanyan Li / Benjamin J Orlando / Maofu Liao / ![]() Abstract: In Gram-negative bacteria, lipopolysaccharide is essential for outer membrane formation and antibiotic resistance. The seven lipopolysaccharide transport (Lpt) proteins A-G move lipopolysaccharide ...In Gram-negative bacteria, lipopolysaccharide is essential for outer membrane formation and antibiotic resistance. The seven lipopolysaccharide transport (Lpt) proteins A-G move lipopolysaccharide from the inner to the outer membrane. The ATP-binding cassette transporter LptBFG, which tightly associates with LptC, extracts lipopolysaccharide out of the inner membrane. The mechanism of the LptBFG-LptC complex (LptBFGC) and the role of LptC in lipopolysaccharide transport are poorly understood. Here we characterize the structures of LptBFG and LptBFGC in nucleotide-free and vanadate-trapped states, using single-particle cryo-electron microscopy. These structures resolve the bound lipopolysaccharide, reveal transporter-lipopolysaccharide interactions with side-chain details and uncover how the capture and extrusion of lipopolysaccharide are coupled to conformational rearrangements of LptBFGC. LptC inserts its transmembrane helix between the two transmembrane domains of LptBFG, which represents a previously unknown regulatory mechanism for ATP-binding cassette transporters. Our results suggest a role for LptC in achieving efficient lipopolysaccharide transport, by coordinating the action of LptBFG in the inner membrane and Lpt protein interactions in 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 | ![]() | 173.4 KB | Display | ![]() |
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PDB format | ![]() | 132.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9124MC ![]() 9118C ![]() 9125C ![]() 9126C ![]() 9128C ![]() 9129C ![]() 9130C ![]() 6mhuC ![]() 6mi7C ![]() 6mi8C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 28131.088 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: lptB, yhbG, b3201, JW3168 / Production host: ![]() ![]() References: UniProt: P0A9V1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances #2: Protein | | Mass: 40393.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 56 Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: lptF, yjgP, b4261, JW4218 / Production host: ![]() ![]() #3: Protein | | Mass: 39651.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: lptG, yjgQ, b4262, JW5760 / Production host: ![]() ![]() #4: Chemical | |
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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: LptB2FG / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: nanodisc incorporated LptB2FG |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55624 / Symmetry type: POINT |