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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20996 | ||||||||||||||||||
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Title | Lipophilic Envelope-spanning Tunnel B (LetB), Map 4 | ||||||||||||||||||
![]() | Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4 (rings 2 to 4, after masking and signal subtraction in Relion) | ||||||||||||||||||
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![]() | conformational dynamics / lipid transport / bacterial cell envelope / LetB / YebT / MCE | ||||||||||||||||||
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: 2.96 Å | ||||||||||||||||||
![]() | Isom GL / Coudray N | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: LetB Structure Reveals a Tunnel for Lipid Transport across the Bacterial Envelope. Authors: Georgia L Isom / Nicolas Coudray / Mark R MacRae / Collin T McManus / Damian C Ekiert / Gira Bhabha / ![]() Abstract: Gram-negative bacteria are surrounded by an outer membrane composed of phospholipids and lipopolysaccharide, which acts as a barrier and contributes to antibiotic resistance. The systems that mediate ...Gram-negative bacteria are surrounded by an outer membrane composed of phospholipids and lipopolysaccharide, which acts as a barrier and contributes to antibiotic resistance. The systems that mediate phospholipid trafficking across the periplasm, such as MCE (Mammalian Cell Entry) transporters, have not been well characterized. Our ~3.5 Å cryo-EM structure of the E. coli MCE protein LetB reveals an ~0.6 megadalton complex that consists of seven stacked rings, with a central hydrophobic tunnel sufficiently long to span the periplasm. Lipids bind inside the tunnel, suggesting that it functions as a pathway for lipid transport. Cryo-EM structures in the open and closed states reveal a dynamic tunnel lining, with implications for gating or substrate translocation. Our results support a model in which LetB establishes a physical link between the two membranes and creates a hydrophobic pathway for the translocation of lipids across the periplasm. | ||||||||||||||||||
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 | ![]() | 50.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.5 KB 13.5 KB | Display Display | ![]() |
Images | ![]() | 86.1 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v0fMC ![]() 6v0cC ![]() 6v0dC ![]() 6v0eC ![]() 6v0gC ![]() 6v0hC ![]() 6v0iC ![]() 6v0jC ![]() 6vciC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Aligned, dose-weighted and non-dose-weighted micrographs [micrographs - single frame] Data #2: Particle stacks for Model 1 (EMD-20993) [picked particles - single frame - processed] Data #3: Particle stacks for Model 2 (EMD-20994) [picked particles - single frame - processed] Data #4: Particle stacks for Model 3 (EMD-20995) [picked particles - single frame - processed] Data #5: Particle stacks for Model 4 (EMD-20996) [picked particles - single frame - processed] Data #6: Particle stacks for Model 5 (EMD-20997) [picked particles - single frame - processed] Data #7: Particle stacks for Model 6 (EMD-20998) [picked particles - single frame - processed] Data #8: Particle stacks for Model 7 (EMD-20999) [picked particles - single frame - processed] Data #9: Particle stacks for Model 8 (EMD-21000) [picked particles - single frame - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4 (rings 2 to 4, after masking and signal subtraction in Relion) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 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 : Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4
Entire | Name: Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4 |
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Components |
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-Supramolecule #1: Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4
Supramolecule | Name: Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Cryo-EM reconstruction of rings 2 to 4, class 2.2.1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 560 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: 89.744031 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 LEKALENSLS DLPTTTVSLS AETLP DVQA GSVVLYRKFE VGEVITVRPR ANAFDIDLHI KPEYRNLLTS NSVFWAEGGA KVQLNGSGLT VQASPLSRAL KGAISF DNL SGASASQRKG DKRILYASET AARAVGGQIT LHAFDAGKLA VGMPIRYLGI DIGQIQTLDL ITARNEVQAK AVLYPEY VQ TFARGGTRFS VVTPQISAAG VEHLDTILQP YINVEPGRGN PRRDFELQEA TITDSRYLDG LSIIVEAPEA GSLGIGTP V LFRGLEVGTV TGMTLGTLSD RVMIAMRISK RYQHLVRNNS VFWLASGYSL DFGLTGGVVK TGTFNQFIRG GIAFATPPG TPLAPKAQEG KHFLLQESEP KEWREWGTAL PK 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
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
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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) / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 4906 / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |