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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0785 | |||||||||
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Title | YebT domain5-7 | |||||||||
![]() | Domain 5-7 of YebT | |||||||||
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![]() | lipid channel / LIPID TRANSPORT | |||||||||
Function / homology | Mce/MlaD / MlaD protein / intermembrane lipid transfer / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane / Intermembrane transport protein YebT![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Wang HW / Liu C | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structure of a Bacterial Lipid Transporter YebT. Authors: Chuan Liu / Jinying Ma / Jia Wang / Hongwei Wang / Li Zhang / ![]() Abstract: The outer membrane (OM) of Gram-negative bacteria is asymmetric, with lipopolysaccharides (LPSs) on the outer surface and phospholipids (PLs) on the inner surface. This unique organization of OM ...The outer membrane (OM) of Gram-negative bacteria is asymmetric, with lipopolysaccharides (LPSs) on the outer surface and phospholipids (PLs) on the inner surface. This unique organization of OM makes Gram-negative bacteria resistant to many toxic chemicals. How this asymmetric distribution of lipids is maintained has been studied for decades with previous reports of an Mla (Maintenance of OM Lipid Asymmetry) system to be involved. Furthermore, the OM of Gram-negative bacteria is about 20 nm away from inner membrane (IM) where the lipids are synthesized. Therefore, how nascent lipids travel across the periplasmic space and arrive at the inner surface of OM is another interesting question. YebT is a homologue of MlaD in the Mla pathway, but its role in lipid distribution of the OM and IM is largely unknown. Here we report the first high-resolution (~3.0 Å) cryo-EM structure of full-length E. coli YebT in a substrate-bound state. Our structure with details of lipid interaction indicates that YebT is a lipid transporter spanning between IM and OM. We also demonstrate the symmetry mismatch in YebT and the existence of many other conformations of YebT revealing the intrinsic dynamics of this lipid channel. And a brief discussion on possible mechanisms of lipid transport is also included. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.4 KB 9.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 101.5 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 363.7 KB | Display | ![]() |
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Full document | ![]() | 363.3 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kz4MC ![]() 0784C ![]() 0786C ![]() 0787C ![]() 0788C ![]() 6kz3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Domain 5-7 of YebT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : YebT-C
Entire | Name: YebT-C |
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Components |
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-Supramolecule #1: YebT-C
Supramolecule | Name: YebT-C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Domain 5-7 of YebT |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Intermembrane transport protein YebT
Macromolecule | Name: Intermembrane transport protein YebT / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 39.542926 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: LPTTTVSLSA ETLPDVQAGS VVLYRKFEVG EVITVRPRAN AFDIDLHIKP EYRNLLTSNS VFWAEGGAKV QLNGSGLTVQ ASPLSRALK GAISFDNLSG ASASQRKGDK RILYASETAA RAVGGQITLH AFDAGKLAVG MPIRYLGIDI GQIQTLDLIT A RNEVQAKA ...String: LPTTTVSLSA ETLPDVQAGS VVLYRKFEVG EVITVRPRAN AFDIDLHIKP EYRNLLTSNS VFWAEGGAKV QLNGSGLTVQ ASPLSRALK GAISFDNLSG ASASQRKGDK RILYASETAA RAVGGQITLH AFDAGKLAVG MPIRYLGIDI GQIQTLDLIT A RNEVQAKA VLYPEYVQTF ARGGTRFSVV TPQISAAGVE HLDTILQPYI NVEPGRGNPR RDFELQEATI TDSRYLDGLS II VEAPEAG SLGIGTPVLF RGLEVGTVTG MTLGTLSDRV MIAMRISKRY QHLVRNNSVF WLASGYSLDF GLTGGVVKTG TFN QFIRGG IAFATPPGTP LAPKAQEGKH FLLQESEPKE WREWGTALPK UniProtKB: Intermembrane transport protein YebT |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |