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- EMDB-20996: Lipophilic Envelope-spanning Tunnel B (LetB), Map 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-20996
TitleLipophilic Envelope-spanning Tunnel B (LetB), Map 4
Map dataLipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4 (rings 2 to 4, after masking and signal subtraction in Relion)
Sample
  • Complex: Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4
    • Protein or peptide: Intermembrane transport protein YebT
Keywordsconformational 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
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsIsom GL / Coudray N
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM112982 United States
Other privateDFS-20-16 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128777-01 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
CitationJournal: Cell / Year: 2020
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
DepositionNov 18, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseMay 6, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v0f
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20996.png

Downloads & links

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Map

FileDownload / File: emd_20996.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4 (rings 2 to 4, after masking and signal subtraction in Relion)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 280 pix.
= 366.8 Å		1.31 Å/pix.
x 280 pix.
= 366.8 Å		1.31 Å/pix.
x 280 pix.
= 366.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.2867189 - 0.5293804
Average (Standard dev.)0.00010996487 (±0.00885437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 366.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z366.800366.800366.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.2870.5290.000

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Supplemental data

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Sample components

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Entire : Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4

EntireName: Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4
Components
  • Complex: Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4
    • Protein or peptide: Intermembrane transport protein YebT

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Supramolecule #1: Lipophilic Envelope-spanning Tunnel B (LetB), Map 4, Model 4

SupramoleculeName: 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
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 560 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 (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 89.744031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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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

Concentration0.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 731231
Startup modelType of model: EMDB MAP
EMDB ID:

8611

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 144219
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 110000 / Software - Name: RELION (ver. 2.1)
Details: Classification of signal subtracted density maps of rings 2 to 4

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Atomic model buiding 1

Initial modelPDB ID:

5uw2


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6v0f:
Lipophilic Envelope-spanning Tunnel B (LetB), Model 4

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