+Open data
-Basic information
Entry | Database: PDB / ID: 4cdi | ||||||
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Title | Crystal structure of AcrB-AcrZ complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / DRUG EFFLUX / TRANSMEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Du, D. / James, N. / Klimont, E. / Luisi, B.F. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Structure of the AcrAB-TolC multidrug efflux pump. Authors: Dijun Du / Zhao Wang / Nathan R James / Jarrod E Voss / Ewa Klimont / Thelma Ohene-Agyei / Henrietta Venter / Wah Chiu / Ben F Luisi / Abstract: The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of ...The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of these transporters form multicomponent 'pumps' that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component. A model system for such a pump is the acridine resistance complex of Escherichia coli. This pump assembly comprises the outer-membrane channel TolC, the secondary transporter AcrB located in the inner membrane, and the periplasmic AcrA, which bridges these two integral membrane proteins. The AcrAB-TolC efflux pump is able to transport vectorially a diverse array of compounds with little chemical similarity, thus conferring resistance to a broad spectrum of antibiotics. Homologous complexes are found in many Gram-negative species, including in animal and plant pathogens. Crystal structures are available for the individual components of the pump and have provided insights into substrate recognition, energy coupling and the transduction of conformational changes associated with the transport process. However, how the subunits are organized in the pump, their stoichiometry and the details of their interactions are not known. Here we present the pseudo-atomic structure of a complete multidrug efflux pump in complex with a modulatory protein partner from E. coli. The model defines the quaternary organization of the pump, identifies key domain interactions, and suggests a cooperative process for channel assembly and opening. These findings illuminate the basis for drug resistance in numerous pathogenic bacterial species. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cdi.cif.gz | 189.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cdi.ent.gz | 146.5 KB | Display | PDB format |
PDBx/mmJSON format | 4cdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cdi_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 4cdi_full_validation.pdf.gz | 467 KB | Display | |
Data in XML | 4cdi_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 4cdi_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/4cdi ftp://data.pdbj.org/pub/pdb/validation_reports/cd/4cdi | HTTPS FTP |
-Related structure data
Related structure data | 5915C 4c48SC S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 113665.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: NOVAGENE / Variant: NOVABLUE ISOLATE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P31224 |
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#2: Protein/peptide | Mass: 5304.423 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: C4ZXT3 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.51 Å3/Da / Density % sol: 72.8 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: THE ACRBZ COMPLEX AT 10 MG ML-1 USING SAMPLE BUFFER. 9 MM N-OCTYL-BETA-D-THIOGLUCOPYRANOSIDE (90 MM) WAS MIXED WITH ACRBZ COMPLEX BEFORE THE CRYSTALLISATION TRIALS. THE ACRBZ CRYSTALS WERE ...Details: THE ACRBZ COMPLEX AT 10 MG ML-1 USING SAMPLE BUFFER. 9 MM N-OCTYL-BETA-D-THIOGLUCOPYRANOSIDE (90 MM) WAS MIXED WITH ACRBZ COMPLEX BEFORE THE CRYSTALLISATION TRIALS. THE ACRBZ CRYSTALS WERE GROWN AT 20 C USING THE HANGING-DROPLET VAPOUR DIFFUSION METHOD BY MIXING 4 MICROLITERS OF ACRBZ COMPLEX WITH 2 MICROLITERS OF RESERVOIR SOLUTION (100 MM TRICINE PH: 7.4, 50 MM LITHIUM SULPHATE, 5 MM CADMIUM CHLORIDE HYDRATE, 7 % PEG 3000, 10% GLYCEROL). |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 3.69→24.89 Å / Num. obs: 23077 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 148 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.1 | |||||||||||||||
Reflection shell | Resolution: 3.69→3.99 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 2.1 / % possible all: 94.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C48 Resolution: 3.7→24.91 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.858 / SU B: 54.668 / SU ML: 0.78 / Cross valid method: THROUGHOUT / ESU R Free: 0.844 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.759 Å2
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Refinement step | Cycle: LAST / Resolution: 3.7→24.91 Å
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