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Yorodumi- PDB-6baj: Cryo-EM structure of lipid bilayer in the native cell membrane na... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6baj | ||||||||||||
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Title | Cryo-EM structure of lipid bilayer in the native cell membrane nanoparticles of AcrB | ||||||||||||
Components | Multidrug efflux pump subunit AcrB | ||||||||||||
Keywords | MEMBRANE PROTEIN / lipid bilayer / native cell membrane nanoparticles system / Resistance-Nodulation-Cell Division (RND) family / phospholipid | ||||||||||||
Function / homology | Function and homology information alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport ...alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Qiu, W. / Fu, Z. / Guo, Y. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Structure and activity of lipid bilayer within a membrane-protein transporter. Authors: Weihua Qiu / Ziao Fu / Guoyan G Xu / Robert A Grassucci / Yan Zhang / Joachim Frank / Wayne A Hendrickson / Youzhong Guo / Abstract: Membrane proteins function in native cell membranes, but extraction into isolated particles is needed for many biochemical and structural analyses. Commonly used detergent-extraction methods destroy ...Membrane proteins function in native cell membranes, but extraction into isolated particles is needed for many biochemical and structural analyses. Commonly used detergent-extraction methods destroy naturally associated lipid bilayers. Here, we devised a detergent-free method for preparing cell-membrane nanoparticles to study the multidrug exporter AcrB, by cryo-EM at 3.2-Å resolution. We discovered a remarkably well-organized lipid-bilayer structure associated with transmembrane domains of the AcrB trimer. This bilayer patch comprises 24 lipid molecules; inner leaflet chains are packed in a hexagonal array, whereas the outer leaflet has highly irregular but ordered packing. Protein side chains interact with both leaflets and participate in the hexagonal pattern. We suggest that the lipid bilayer supports and harmonizes peristaltic motions through AcrB trimers. In AcrB D407A, a putative proton-relay mutant, lipid bilayer buttresses protein interactions lost in crystal structures after detergent-solubilization. Our detergent-free system preserves lipid-protein interactions for visualization and should be broadly applicable. | ||||||||||||
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 | 6baj.cif.gz | 543 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6baj.ent.gz | 445.9 KB | Display | PDB format |
PDBx/mmJSON format | 6baj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6baj_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6baj_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6baj_validation.xml.gz | 92.2 KB | Display | |
Data in CIF | 6baj_validation.cif.gz | 133.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/6baj ftp://data.pdbj.org/pub/pdb/validation_reports/ba/6baj | HTTPS FTP |
-Related structure data
Related structure data | 7074MC 7609C 6csxC 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
#1: Protein | Mass: 114736.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224 #2: Chemical | ChemComp-PTY / #3: Chemical | ChemComp-D12 / #4: Water | ChemComp-HOH / | |
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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: Native cell membrane nanoparticles of AcrB / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: BRIGHT FIELD |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57395 / Symmetry type: POINT |