+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8467 | |||||||||
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Title | Cryo-EM structure of MsbA-nanodisc with ADP-vanadate | |||||||||
Map data | 3D cryo-EM density map of MsbA-nanodisc with ADP-vanadate | |||||||||
Sample |
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Keywords | ABC transporter / LPS / flippase / nanodisc / HYDROLASE | |||||||||
Function / homology | Function and homology information ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli O157:H7 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Mi W / Walz T | |||||||||
Citation | Journal: Nature / Year: 2017 Title: Structural basis of MsbA-mediated lipopolysaccharide transport. Authors: Wei Mi / Yanyan Li / Sung Hwan Yoon / Robert K Ernst / Thomas Walz / Maofu Liao / Abstract: Lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria is critical for the assembly of their cell envelopes. LPS synthesized in the cytoplasmic leaflet of the inner membrane is ...Lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria is critical for the assembly of their cell envelopes. LPS synthesized in the cytoplasmic leaflet of the inner membrane is flipped to the periplasmic leaflet by MsbA, an ATP-binding cassette transporter. Despite substantial efforts, the structural mechanisms underlying MsbA-driven LPS flipping remain elusive. Here we use single-particle cryo-electron microscopy to elucidate the structures of lipid-nanodisc-embedded MsbA in three functional states. The 4.2 Å-resolution structure of the transmembrane domains of nucleotide-free MsbA reveals that LPS binds deep inside MsbA at the height of the periplasmic leaflet, establishing extensive hydrophilic and hydrophobic interactions with MsbA. Two sub-nanometre-resolution structures of MsbA with ADP-vanadate and ADP reveal an unprecedented closed and an inward-facing conformation, respectively. Our study uncovers the structural basis for LPS recognition, delineates the conformational transitions of MsbA to flip LPS, and paves the way for structural characterization of other lipid flippases. | |||||||||
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_8467.map.gz | 24.9 MB | EMDB map data format | |
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Header (meta data) | emd-8467-v30.xml emd-8467.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8467_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_8467.png | 33.4 KB | ||
Filedesc metadata | emd-8467.cif.gz | 5.2 KB | ||
Others | emd_8467_additional.map.gz | 19.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8467 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8467 | HTTPS FTP |
-Validation report
Summary document | emd_8467_validation.pdf.gz | 554.6 KB | Display | EMDB validaton report |
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Full document | emd_8467_full_validation.pdf.gz | 554.2 KB | Display | |
Data in XML | emd_8467_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | emd_8467_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8467 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8467 | HTTPS FTP |
-Related structure data
Related structure data | 5ttpMC 8465C 8469C 8669C 8670C 8671C 5tv4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_8467.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D cryo-EM density map of MsbA-nanodisc with ADP-vanadate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 3D cryo-EM density map of MsbA-nanodisc with ADP-vanadate,...
File | emd_8467_additional.map | ||||||||||||
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Annotation | 3D cryo-EM density map of MsbA-nanodisc with ADP-vanadate, without low-pass filter or amplitude modification | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : MsbA reconstituted in lipid nanodiscs
Entire | Name: MsbA reconstituted in lipid nanodiscs |
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Components |
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-Supramolecule #1: MsbA reconstituted in lipid nanodiscs
Supramolecule | Name: MsbA reconstituted in lipid nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Lipid A export ATP-binding/permease protein MsbA
Macromolecule | Name: Lipid A export ATP-binding/permease protein MsbA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
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Source (natural) | Organism: Escherichia coli O157:H7 (bacteria) |
Molecular weight | Theoretical: 67.310445 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MGHHHHHHHH HHSSGHIDDD DKHMHNDKDL STWQTFRRLW PTIAPFKAGL IVAGVALILN AASDTFMLSL LKPLLDDGFG KTDRSVLVW MPLVVIGLMI LRGITSYVSS YCISWVSGKV VMTMRRRLFG HMMGMPVSFF DKQSTGTLLS RITYDSEQVA S SSSGALIT ...String: MGHHHHHHHH HHSSGHIDDD DKHMHNDKDL STWQTFRRLW PTIAPFKAGL IVAGVALILN AASDTFMLSL LKPLLDDGFG KTDRSVLVW MPLVVIGLMI LRGITSYVSS YCISWVSGKV VMTMRRRLFG HMMGMPVSFF DKQSTGTLLS RITYDSEQVA S SSSGALIT VVREGASIIG LFIMMFYYSW QLSIILIVLA PIVSIAIRVV SKRFRNISKN MQNTMGQVTT SAEQMLKGHK EV LIFGGQE VETKRFDKVS NRMRLQGMKM VSASSISDPI IQLIASLALA FVLYAASFPS VMDSLTAGTI TVVFSSMIAL MRP LKSLTN VNAQFQRGMA ACQTLFTILD SEQEKDEGKR VIERATGDVE FRNVTFTYPG RDVPALRNIN LKIPAGKTVA LVGR SGSGK STIASLITRF YDIDEGEILM DGHDLREYTL ASLRNQVALV SQNVHLFNDT VANNIAYART EQYSREQIEE AARMA YAMD FINKMDNGLD TVIGENGVLL SGGQRQRIAI ARALLRDSPI LILDEATSAL DTESERAIQA ALDELQKNRT SLVIAH RLS TIEKADEIVV VEDGVIVERG THNDLLEHRG VYAQLHKMQF GQ UniProtKB: ATP-dependent lipid A-core flippase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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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: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |