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- EMDB-9130: Cryo-EM Structure of E.coli LptB2FGC with short BJR -

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Basic information

Entry
Database: EMDB / ID: EMD-9130
TitleCryo-EM Structure of E.coli LptB2FGC with short BJR
Map dataCryo-EM map of LptB2FGC with short BJR, filtered to 5.9A and -300 b-factor
Sample
  • Complex: LptB2FGC
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsOrlando BJ / Li Y / Liao M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesR01GM122797 United States
CitationJournal: Nature / Year: 2019
Title: Structural basis of lipopolysaccharide extraction by the LptBFGC complex.
Authors: Yanyan Li / Benjamin J Orlando / Maofu Liao /
Abstract: In Gram-negative bacteria, lipopolysaccharide is essential for outer membrane formation and antibiotic resistance. The seven lipopolysaccharide transport (Lpt) proteins A-G move lipopolysaccharide ...In Gram-negative bacteria, lipopolysaccharide is essential for outer membrane formation and antibiotic resistance. The seven lipopolysaccharide transport (Lpt) proteins A-G move lipopolysaccharide from the inner to the outer membrane. The ATP-binding cassette transporter LptBFG, which tightly associates with LptC, extracts lipopolysaccharide out of the inner membrane. The mechanism of the LptBFG-LptC complex (LptBFGC) and the role of LptC in lipopolysaccharide transport are poorly understood. Here we characterize the structures of LptBFG and LptBFGC in nucleotide-free and vanadate-trapped states, using single-particle cryo-electron microscopy. These structures resolve the bound lipopolysaccharide, reveal transporter-lipopolysaccharide interactions with side-chain details and uncover how the capture and extrusion of lipopolysaccharide are coupled to conformational rearrangements of LptBFGC. LptC inserts its transmembrane helix between the two transmembrane domains of LptBFG, which represents a previously unknown regulatory mechanism for ATP-binding cassette transporters. Our results suggest a role for LptC in achieving efficient lipopolysaccharide transport, by coordinating the action of LptBFG in the inner membrane and Lpt protein interactions in the periplasm.
History
DepositionSep 19, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseApr 3, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9130.png

Downloads & links

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Map

FileDownload / File: emd_9130.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of LptB2FGC with short BJR, filtered to 5.9A and -300 b-factor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 192 pix.
= 236.16 Å		1.23 Å/pix.
x 192 pix.
= 236.16 Å		1.23 Å/pix.
x 192 pix.
= 236.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.07886847 - 0.16416392
Average (Standard dev.)0.000010365165 (±0.006559631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 236.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z236.160236.160236.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.0790.1640.000

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Supplemental data

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Additional map: unfiltered cryo-EM map of LptB2FGC with short BJR

Fileemd_9130_additional.map
Annotationunfiltered cryo-EM map of LptB2FGC with short BJR
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LptB2FGC

EntireName: LptB2FGC
Components
  • Complex: LptB2FGC

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Supramolecule #1: LptB2FGC

SupramoleculeName: LptB2FGC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration4 mg/mL
BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE
Detailsnanodisc incorporated LptB2FGC

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66375
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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