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- EMDB-0786: Cryo-EM Structure of YebT in conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0786
TitleCryo-EM Structure of YebT in conformation 1
Map dataThe whole map of YebT
Sample
  • Complex: YebT
    • Protein or peptide: YebT
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsLiu C / Zhang L / Wang HW / Wang J / Li XM
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-
UpdateMar 11, 2020-
Current statusMar 11, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0786.png

Downloads & links

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Map

FileDownload / File: emd_0786.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe whole map 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: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.01784045 - 0.050928753
Average (Standard dev.)0.00014984707 (±0.0014975772)
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
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0180.0510.000

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Supplemental data

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Sample components

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Entire : YebT

EntireName: YebT
Components
  • Complex: YebT
    • Protein or peptide: YebT

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Supramolecule #1: YebT

SupramoleculeName: YebT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Full length YebT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 570 KDa

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Macromolecule #1: YebT

MacromoleculeName: YebT / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
SequenceString: MSQETPASTT EAQIKNKRRI SPFWLLPFIA LMIASWLIWD SYQDRGNTVT IDFMSADGIV PGRTPVRYQ GVEVGTVQDI SLSDDLRKIE VKVSIKSDMK DALREETQFW LVTPKASLAG V SGLDALVG GNYIGMMPGK GKEQDHFVAL DTQPKYRLDN GDLMIHLQAP ...String:
MSQETPASTT EAQIKNKRRI SPFWLLPFIA LMIASWLIWD SYQDRGNTVT IDFMSADGIV PGRTPVRYQ GVEVGTVQDI SLSDDLRKIE VKVSIKSDMK DALREETQFW LVTPKASLAG V SGLDALVG GNYIGMMPGK GKEQDHFVAL DTQPKYRLDN GDLMIHLQAP DLGSLNSGSL VY FRKIPVG KVYDYAINPN KQGVVIDVLI ERRFTDLVKK GSRFWNVSGV DANVSISGAK VKL ESLAAL VNGAIAFDSP EESKPAEAED TFGLYEDLAH SQRGVIIKLE LPSGAGLTAD STPL MYQGL EVGQLTKLDL NPGGKVTGEM TVDPSVVTLL RENTRIELRN PKLSLSDANL SALLT GKTF ELVPGDGEPR KEFVVVPGEK ALLHEPDVLT LTLTAPESYG IDAGQPLILH GVQVGQ VID RKLTSKGVTF TVAIEPQHRE LVKGDSKFVV NSRVDVKVGL DGVEFLGASA SEWINGG IR ILPGDKGEMK ASYPLYANLE KALENSLSDL PTTTVSLSAE TLPDVQAGSV VLYRKFEV G EVITVRPRAN AFDIDLHIKP EYRNLLTSNS VFWAEGGAKV QLNGSGLTVQ ASPLSRALK GAISFDNLSG ASASQRKGDK RILYASETAA RAVGGQITLH AFDAGKLAVG MPIRYLGIDI GQIQTLDLI TARNEVQAKA VLYPEYVQTF ARGGTRFSVV TPQISAAGVE HLDTILQPYI N VEPGRGNP RRDFELQEAT ITDSRYLDGL SIIVEAPEAG SLGIGTPVLF RGLEVGTVTG MT LGTLSDR VMIAMRISKR YQHLVRNNSV FWLASGYSLD FGLTGGVVKT GTFNQFIRGG IAF ATPPGT PLAPKAQEGK HFLLQESEPK EWREWGTALP K

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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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 420134
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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