+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24446 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | E. coli MsbA in complex with G247 in DDM, C2 map | |||||||||
Map data | E. coli MsbA in complex with G247 in DDM, C2 map | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.55 Å | |||||||||
Authors | Thelot F / Liao M | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Science / Year: 2021 Title: Distinct allosteric mechanisms of first-generation MsbA inhibitors. Authors: François A Thélot / Wenyi Zhang / KangKang Song / Chen Xu / Jing Huang / Maofu Liao / Abstract: ATP-binding cassette (ABC) transporters couple adenosine 5′-triphosphate (ATP) hydrolysis to substrate transport across biological membranes. Although many are promising drug targets, their ...ATP-binding cassette (ABC) transporters couple adenosine 5′-triphosphate (ATP) hydrolysis to substrate transport across biological membranes. Although many are promising drug targets, their mechanisms of modulation by small-molecule inhibitors remain largely unknown. Two first-generation inhibitors of the MsbA transporter, tetrahydrobenzothiophene 1 (TBT1) and G247, induce opposite effects on ATP hydrolysis. Using single-particle cryo–electron microscopy and functional assays, we show that TBT1 and G247 bind adjacent yet separate pockets in the MsbA transmembrane domains. Two TBT1 molecules asymmetrically occupy the substrate-binding site, which leads to a collapsed inward-facing conformation with decreased distance between the nucleotide-binding domains (NBDs). By contrast, two G247 molecules symmetrically increase NBD distance in a wide inward-open state of MsbA. The divergent mechanisms of action of these MsbA inhibitors provide important insights into ABC transporter pharmacology. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24446.map.gz | 5.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-24446-v30.xml emd-24446.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_24446.png | 88.3 KB | ||
Others | emd_24446_additional_1.map.gz | 19.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24446 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24446 | HTTPS FTP |
-Validation report
Summary document | emd_24446_validation.pdf.gz | 300.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_24446_full_validation.pdf.gz | 300.5 KB | Display | |
Data in XML | emd_24446_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_24446_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24446 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24446 | HTTPS FTP |
-Related structure data
Related structure data | 7metC 7mewC 7ritC C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10800 (Title: E. coli MsbA in DDM in complex with G247 / Data size: 307.0 Data #1: E. coli MsbA in DDM in complex with G247 [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_24446.map.gz / Format: CCP4 / Size: 6.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | E. coli MsbA in complex with G247 in DDM, C2 map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: unfiltered, unsharpened map for E. coli MsbA in...
File | emd_24446_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unfiltered, unsharpened map for E. coli MsbA in complex with G247 in DDM, C2 map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : E. coli MsbA in complex with G247 in DDM, C2 map
Entire | Name: E. coli MsbA in complex with G247 in DDM, C2 map |
---|---|
Components |
|
-Supramolecule #1: E. coli MsbA in complex with G247 in DDM, C2 map
Supramolecule | Name: E. coli MsbA in complex with G247 in DDM, C2 map / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 130 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 16 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 942315 |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |