+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0784 | |||||||||
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Title | YebT domain1-4 | |||||||||
Map data | The N-terminal part of YebT containing domain 1, domain 2, domain 3 and domain 4. | |||||||||
Sample |
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Keywords | 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 Function and homology information | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Wang HW / Liu C | |||||||||
Funding support | China, 2 items
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Citation | Journal: J Mol Biol / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0784.map.gz | 11.6 MB | EMDB map data format | |
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Header (meta data) | emd-0784-v30.xml emd-0784.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0784_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_0784.png | 55.9 KB | ||
Filedesc metadata | emd-0784.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0784 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0784 | HTTPS FTP |
-Validation report
Summary document | emd_0784_validation.pdf.gz | 366.5 KB | Display | EMDB validaton report |
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Full document | emd_0784_full_validation.pdf.gz | 366.1 KB | Display | |
Data in XML | emd_0784_validation.xml.gz | 13 KB | Display | |
Data in CIF | emd_0784_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0784 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0784 | HTTPS FTP |
-Related structure data
Related structure data | 6kz3MC 0785C 0786C 0787C 0788C 6kz4C 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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-Map
File | Download / File: emd_0784.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The N-terminal part of YebT containing domain 1, domain 2, domain 3 and domain 4. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : YebT-N
Entire | Name: YebT-N |
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Components |
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-Supramolecule #1: YebT-N
Supramolecule | Name: YebT-N / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Domain 1-4 of YebT |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
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: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 50.016824 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: GNTVTIDFMS ADGIVPGRTP VRYQGVEVGT VQDISLSDDL RKIEVKVSIK SDMKDALREE TQFWLVTPKA SLAGVSGLDA LVGGNYIGM MPGKGKEQDH FVALDTQPKY RLDNGDLMIH LQAPDLGSLN SGSLVYFRKI PVGKVYDYAI NPNKQGVVID V LIERRFTD ...String: GNTVTIDFMS ADGIVPGRTP VRYQGVEVGT VQDISLSDDL RKIEVKVSIK SDMKDALREE TQFWLVTPKA SLAGVSGLDA LVGGNYIGM MPGKGKEQDH FVALDTQPKY RLDNGDLMIH LQAPDLGSLN SGSLVYFRKI PVGKVYDYAI NPNKQGVVID V LIERRFTD LVKKGSRFWN VSGVDANVSI SGAKVKLESL AALVNGAIAF DSPEESKPAE AEDTFGLYED LAHSQRGVII KL ELPSGAG LTADSTPLMY QGLEVGQLTK LDLNPGGKVT GEMTVDPSVV TLLRENTRIE LRNPKLSLSD ANLSALLTGK TFE LVPGDG EPRKEFVVVP GEKALLHEPD VLTLTLTAPE SYGIDAGQPL ILHGVQVGQV IDRKLTSKGV TFTVAIEPQH RELV KGDSK FVVNSRVDVK VGLDGVEFLG ASASEWINGG IRILPGDKGE MKASYPLYAN LEKALENSL UniProtKB: Intermembrane transport protein YebT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 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: Titan Krios / Image courtesy: FEI Company |