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Yorodumi- PDB-7kf7: Cryo-electron microscopy structure of the heavy metal efflux pump... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kf7 | ||||||
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Title | Cryo-electron microscopy structure of the heavy metal efflux pump CusA in a heterogeneous 1 open and 2 closed protomer conformation | ||||||
Components | Cation efflux system protein CusA | ||||||
Keywords | MEMBRANE PROTEIN/ TRANSPORT PROTEIN / efflux / pump / heavy metal. copper / silver / closed / open / transporter / MEMBRANE PROTEIN / MEMBRANE PROTEIN- TRANSPORT PROTEIN complex | ||||||
Function / homology | Function and homology information silver ion transmembrane transporter activity / silver ion transport / plasma membrane copper ion transport / silver ion transmembrane transport / copper ion transmembrane transport / response to silver ion / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion ...silver ion transmembrane transporter activity / silver ion transport / plasma membrane copper ion transport / silver ion transmembrane transport / copper ion transmembrane transport / response to silver ion / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion / xenobiotic transmembrane transporter activity / intracellular copper ion homeostasis / response to toxic substance / copper ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Moseng, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: mBio / Year: 2021 Title: Cryo-EM Structures of CusA Reveal a Mechanism of Metal-Ion Export. Authors: Mitchell A Moseng / Meinan Lyu / Tanadet Pipatpolkai / Przemyslaw Glaza / Corey C Emerson / Phoebe L Stewart / Phillip J Stansfeld / Edward W Yu / Abstract: Gram-negative bacteria utilize the resistance-nodulation-cell division (RND) superfamily of efflux pumps to expel a variety of toxic compounds from the cell. The CusA membrane protein, which ...Gram-negative bacteria utilize the resistance-nodulation-cell division (RND) superfamily of efflux pumps to expel a variety of toxic compounds from the cell. The CusA membrane protein, which recognizes and extrudes biocidal Cu(I) and Ag(I) ions, belongs to the heavy-metal efflux (HME) subfamily of RND efflux pumps. We here report four structures of the trimeric CusA heavy-metal efflux pump in the presence of Cu(I) using single-particle cryo-electron microscopy (cryo-EM). We discover that different CusA protomers within the trimer are able to bind Cu(I) ions simultaneously. Our structural data combined with molecular dynamics (MD) simulations allow us to propose a mechanism for ion transport where each CusA protomer functions independently within the trimer. The bacterial RND superfamily of efflux pumps mediate resistance to a variety of biocides, including Cu(I) and Ag(I) ions. Here we report four cryo-EM structures of the trimeric CusA pump in the presence of Cu(I). Combined with MD simulations, our data indicate that each CusA protomer within the trimer recognizes and extrudes Cu(I) independently. | ||||||
History |
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-Structure visualization
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Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7kf7.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7kf7.ent.gz | 963.4 KB | Display | PDB format |
PDBx/mmJSON format | 7kf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kf7_validation.pdf.gz | 924.4 KB | Display | wwPDB validaton report |
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Full document | 7kf7_full_validation.pdf.gz | 948.5 KB | Display | |
Data in XML | 7kf7_validation.xml.gz | 74.4 KB | Display | |
Data in CIF | 7kf7_validation.cif.gz | 115.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/7kf7 ftp://data.pdbj.org/pub/pdb/validation_reports/kf/7kf7 | HTTPS FTP |
-Related structure data
Related structure data | 22845MC 7kf5C 7kf6C 7kf8C 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: 115833.945 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cusA, ybdE, b0575, JW0564 / Production host: Escherichia coli (E. coli) / References: UniProt: P38054 #2: Chemical | ChemComp-CU1 / | Has ligand of interest | Y | |
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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: CusA with heterogeneous protomer conformations / 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 |
Specimen | 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 I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.5 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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75703 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |