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Yorodumi- EMDB-11083: Cryo-EM structure of the Acinetobacter baumannii MlaBDEF complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11083 | |||||||||
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Title | Cryo-EM structure of the Acinetobacter baumannii MlaBDEF complex | |||||||||
Map data | map of the Acinetobacter baumannii MlaBDEF complex to 4.2 A | |||||||||
Sample |
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Function / homology | Function and homology information phospholipid transporter activity / ATP-binding cassette (ABC) transporter complex / phospholipid binding / extracellular region / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.24 Å | |||||||||
Authors | Mann D / Bergeron JRC | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Commun Biol / Year: 2021 Title: Structure and lipid dynamics in the maintenance of lipid asymmetry inner membrane complex of A. baumannii. Authors: Daniel Mann / Junping Fan / Kamolrat Somboon / Daniel P Farrell / Andrew Muenks / Svetomir B Tzokov / Frank DiMaio / Syma Khalid / Samuel I Miller / Julien R C Bergeron / Abstract: Multi-resistant bacteria are a major threat in modern medicine. The gram-negative coccobacillus Acinetobacter baumannii currently leads the WHO list of pathogens in critical need for new therapeutic ...Multi-resistant bacteria are a major threat in modern medicine. The gram-negative coccobacillus Acinetobacter baumannii currently leads the WHO list of pathogens in critical need for new therapeutic development. The maintenance of lipid asymmetry (MLA) protein complex is one of the core machineries that transport lipids from/to the outer membrane in gram-negative bacteria. It also contributes to broad-range antibiotic resistance in several pathogens, most prominently in A. baumannii. Nonetheless, the molecular details of its role in lipid transport has remained largely elusive. Here, we report the cryo-EM maps of the core MLA complex, MlaBDEF, from the pathogen A. baumannii, in the apo-, ATP- and ADP-bound states, revealing multiple lipid binding sites in the cytosolic and periplasmic side of the complex. Molecular dynamics simulations suggest their potential trajectory across the membrane. Collectively with the recently-reported structures of the E. coli orthologue, this data also allows us to propose a molecular mechanism of lipid transport by the MLA system. #1: Journal: Biorxiv / Year: 2020 Title: Structure and lipid dynamics in the A. baumannii maintenance of lipid asymmetry (MLA) inner membrane complex Authors: Mann D / Fan J / Farrell DP / Somboon K / Muenks A / Tzokov SB / Khalid S / Dimaio F / Miller SI / Bergeron JRC | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11083.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-11083-v30.xml emd-11083.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_11083.png | 113.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11083 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11083 | HTTPS FTP |
-Validation report
Summary document | emd_11083_validation.pdf.gz | 230.3 KB | Display | EMDB validaton report |
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Full document | emd_11083_full_validation.pdf.gz | 229.4 KB | Display | |
Data in XML | emd_11083_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_11083_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11083 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11083 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11083.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map of the Acinetobacter baumannii MlaBDEF complex to 4.2 A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : MlaBDEF
Entire | Name: MlaBDEF |
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Components |
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-Supramolecule #1: MlaBDEF
Supramolecule | Name: MlaBDEF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28699 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |