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Yorodumi- EMDB-11082: Cryo-EM structure of the A. baumannii MlaBDEF complex bound to APPNHP -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11082 | |||||||||
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Title | Cryo-EM structure of the A. baumannii MlaBDEF complex bound to APPNHP | |||||||||
Map data | Map of the A. baumannii MlaBDEF complex, bound to APPNHP, at 3.9A resolution. | |||||||||
Sample |
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Keywords | lipid transport / antibiotic resistance / ABC transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information phospholipid transporter activity / ATP-binding cassette (ABC) transporter complex / phospholipid binding / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 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_11082.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-11082-v30.xml emd-11082.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_11082.png | 168.6 KB | ||
Masks | emd_11082_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-11082.cif.gz | 6.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11082 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11082 | HTTPS FTP |
-Validation report
Summary document | emd_11082_validation.pdf.gz | 291.9 KB | Display | EMDB validaton report |
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Full document | emd_11082_full_validation.pdf.gz | 291 KB | Display | |
Data in XML | emd_11082_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_11082_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11082 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11082 | HTTPS FTP |
-Related structure data
Related structure data | 6z5uMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10425 (Title: Cryo-EM structure of the A.baumannii MlaBDEF complex bound to AppNHp Data size: 135.6 Data #1: MotionCor2 aligned micrographs [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11082.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of the A. baumannii MlaBDEF complex, bound to APPNHP, at 3.9A resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11082_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : MlaBDEF complex
Entire | Name: MlaBDEF complex |
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Components |
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-Supramolecule #1: MlaBDEF complex
Supramolecule | Name: MlaBDEF complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
-Macromolecule #1: ABC transporter permease
Macromolecule | Name: ABC transporter permease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Molecular weight | Theoretical: 27.322443 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK ...String: MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK LVGVDFLGVD EGSFWSGMQN NVQFGHDVVN GIIKSIVFAL LCTWIAVFQG YACDPTPEGI ATAMTRTVVY SS LCVLGFD FVLTAVMFGG I UniProtKB: Intermembrane phospholipid transport system permease protein MlaE |
-Macromolecule #2: Anti-sigma factor antagonist
Macromolecule | Name: Anti-sigma factor antagonist / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Molecular weight | Theoretical: 10.874672 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MVQYLNQELV VSGKIDFENA EQQYQAGLAI IKKQTSFPLI VDLKQLEHGN TLALAVLVQW LRQTPQKSGL HFKNVPEKML KIIQACHLQ EDLHLV UniProtKB: Anti-sigma factor antagonist |
-Macromolecule #3: MCE family protein
Macromolecule | Name: MCE family protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Molecular weight | Theoretical: 24.135322 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN ...String: MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN YLKRGDTISN TQGTMDLEDL ISKFITGGGA GKVAAGSSSA EEKAPASTDS SAQPSFVE UniProtKB: ABC transporter periplasmic substrate-binding protein |
-Macromolecule #4: ABC transporter ATP-binding protein
Macromolecule | Name: ABC transporter ATP-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Molecular weight | Theoretical: 30.367848 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIAIMNNKTP LSTQSLIEVK NLSFNRGERV IYDNISLNIR RGQITAIMGP SGTGKTTLLR LIGGQLVPDQ GEVLLDGKDI AQMSRQELF AARARMGMLF QSGALFTDMS VYENVAFPIR AHTKLSENLI AELVALKLES VGLRGTEQLM PTELSGGMNR R VALARAIA ...String: MIAIMNNKTP LSTQSLIEVK NLSFNRGERV IYDNISLNIR RGQITAIMGP SGTGKTTLLR LIGGQLVPDQ GEVLLDGKDI AQMSRQELF AARARMGMLF QSGALFTDMS VYENVAFPIR AHTKLSENLI AELVALKLES VGLRGTEQLM PTELSGGMNR R VALARAIA LDPDLIMYDE PFAGQDPIVK GVLTRLIRSL REALDLTTII VSHDVPETLS IADYIYVVAE GKIQGEGTPE EL QAYASPF VKQFLTGSAE GPVEYQFSHQ AYLDNEVRP UniProtKB: ABC transporter ATP-binding protein |
-Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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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 K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 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
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93295 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |