+Open data
-Basic information
Entry | Database: PDB / ID: 6s8n | ||||||
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Title | Cryo-EM structure of LptB2FGC in complex with lipopolysaccharide | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / lipopolysaccharide transporter / LPS / LptB2FGC / LptB / LptBFG / outer membrane / Gram-negative bacteria / ABC transporter / Inner membrane protein complex | ||||||
Function / homology | Function and homology information lipopolysaccharide transmembrane transporter activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / plasma membrane => GO:0005886 / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Tang, X.D. / Chang, S.H. / Luo, Q.H. / Zhang, Z.Y. / Qiao, W. / Xu, C.H. / Zhang, C.B. / Niu, Y. / Yang, W.X. / Wang, T. ...Tang, X.D. / Chang, S.H. / Luo, Q.H. / Zhang, Z.Y. / Qiao, W. / Xu, C.H. / Zhang, C.B. / Niu, Y. / Yang, W.X. / Wang, T. / Zhang, Z.B. / Zhu, X.F. / Dong, C.J. / Zhang, X. / Dong, H.H. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Cryo-EM structures of lipopolysaccharide transporter LptBFGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism. Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / ...Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong / Abstract: Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through ...Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through a bridge formed by seven membrane proteins (LptBFGCADE). The IM component LptBFG powers the process through a yet unclarified mechanism. Here we report three high-resolution cryo-EM structures of LptBFG alone and complexed with LptC (LptBFGC), trapped in either the LPS- or AMP-PNP-bound state. The structures reveal conformational changes between these states and substrate binding with or without LptC. We identify two functional transmembrane arginine-containing loops interacting with the bound AMP-PNP and elucidate allosteric communications between the domains. AMP-PNP binding induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge. Functional assays reveal the functionality of the LptF and LptG periplasmic domains. Our findings shed light on the LPS transport mechanism. #1: Journal: Nat Commun / Year: 2019 Title: Cryo-EM structures of lipopolysaccharide transporter LptBFGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism. Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / ...Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong / Abstract: Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through ...Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through a bridge formed by seven membrane proteins (LptBFGCADE). The IM component LptBFG powers the process through a yet unclarified mechanism. Here we report three high-resolution cryo-EM structures of LptBFG alone and complexed with LptC (LptBFGC), trapped in either the LPS- or AMP-PNP-bound state. The structures reveal conformational changes between these states and substrate binding with or without LptC. We identify two functional transmembrane arginine-containing loops interacting with the bound AMP-PNP and elucidate allosteric communications between the domains. AMP-PNP binding induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge. Functional assays reveal the functionality of the LptF and LptG periplasmic domains. Our findings shed light on the LPS transport mechanism. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s8n.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s8n.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 6s8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/6s8n ftp://data.pdbj.org/pub/pdb/validation_reports/s8/6s8n | HTTPS FTP |
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-Related structure data
Related structure data | 10125MC 6s8gC 6s8hC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 3 molecules ABG
#1: Protein | Mass: 26837.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: SGF_01136 / Production host: Escherichia coli (E. coli) / References: UniProt: E7T9E6, UniProt: P0A9V4*PLUS #4: Protein | | Mass: 39622.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) Gene: yjgQ, S4488, CQA91_25110, NCTC9783_00309, SAMEA3710568_03584 Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S4N3I3, UniProt: A0A0H2V3J7*PLUS |
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-Lipopolysaccharide export system ... , 2 types, 2 molecules CF
#2: Protein | Mass: 21726.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: lptC, SFxv_3552 / Production host: Escherichia coli (E. coli) / References: UniProt: D2A8C1, UniProt: P0ADW2*PLUS |
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#3: Protein | Mass: 40345.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: lptF, SF4228, S4489 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFA1 |
-Sugars , 1 types, 2 molecules
#7: Sugar |
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-Non-polymers , 3 types, 5 molecules
#5: Chemical | #6: Chemical | #8: Chemical | ChemComp-L0W / | |
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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 |
-Sample preparation
Component | Name: LptB2FGC / Type: COMPLEX / Details: LPS transporter LptB2FGC / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||||||
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Source (natural) | Organism: Shigella flexneri (bacteria) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 546301 / Symmetry type: POINT |