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- EMDB-0785: YebT domain5-7 -

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Basic information

Entry
Database: EMDB / ID: EMD-0785
TitleYebT domain5-7
Map dataDomain 5-7 of YebT
Sample
  • Complex: YebT-C
    • Protein or peptide: Intermembrane transport protein YebT
Keywordslipid channel / LIPID TRANSPORT
Function / homology: / Mce/MlaD / MlaD protein / intermembrane lipid transfer / membrane organization / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane / Lipophilic envelope-spanning tunnel protein B
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang HW / Liu C
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China) China
National Natural Science Foundation of China China
CitationJournal: 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
DepositionSep 23, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kz4
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0785.png

Downloads & links

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Map

FileDownload / File: emd_0785.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDomain 5-7 of YebT
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 360 pix.
= 478.8 Å		1.33 Å/pix.
x 360 pix.
= 478.8 Å		1.33 Å/pix.
x 360 pix.
= 478.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.08607409 - 0.15706371
Average (Standard dev.)0.000055676566 (±0.0020806063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 478.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z478.800478.800478.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0860.1570.000

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Supplemental data

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Sample components

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Entire : YebT-C

EntireName: YebT-C
Components
  • Complex: YebT-C
    • Protein or peptide: Intermembrane transport protein YebT

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Supramolecule #1: YebT-C

SupramoleculeName: YebT-C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Domain 5-7 of YebT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Intermembrane transport protein YebT

MacromoleculeName: Intermembrane transport protein YebT / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 39.542926 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: 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: Lipophilic envelope-spanning tunnel protein B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114211
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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