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- EMDB-3887: AcrB in a SMALP -

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Basic information

Entry
Database: EMDB / ID: EMD-3887
TitleAcrB in a SMALP
Map dataAcrB in SMA polymer. Map filtered by local resolution in RELION 2.1
Sample
  • Complex: Escherichia coli multidrug efflux transporter AcrB in a SMALP platform
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsParmar M / Rawson S / Scarff CA / Goldman A / Dafforn TR / Muench SP / Postis VLG
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2018
Title: Using a SMALP platform to determine a sub-nm single particle cryo-EM membrane protein structure.
Authors: Mayuriben Parmar / Shaun Rawson / Charlotte A Scarff / Adrian Goldman / Timothy R Dafforn / Stephen P Muench / Vincent L G Postis /
Abstract: The field of membrane protein structural biology has been revolutionized over the last few years with a number of high profile structures being solved using cryo-EM including Piezo, Ryanodine ...The field of membrane protein structural biology has been revolutionized over the last few years with a number of high profile structures being solved using cryo-EM including Piezo, Ryanodine receptor, TRPV1 and the Glutamate receptor. Further developments in the EM field hold the promise of even greater progress in terms of greater resolution, which for membrane proteins is still typically within the 4-7Å range. One advantage of a cryo-EM approach is the ability to study membrane proteins in more "native" like environments for example proteoliposomes, amphipols and nanodiscs. Recently, styrene maleic acid co-polymers (SMA) have been used to extract membrane proteins surrounded by native lipids (SMALPs) maintaining a more natural environment. We report here the structure of the Escherichia coli multidrug efflux transporter AcrB in a SMALP scaffold to sub-nm resolution, with the resulting map being consistent with high resolution crystal structures and other EM derived maps. However, both the C-terminal helix (TM12) and TM7 are poorly defined in the map. These helices are at the exterior of the helical bundle and form the greater interaction with the native lipids and SMA polymer and may represent a more dynamic region of the protein. This work shows the promise of using an SMA approach for single particle cryo-EM studies to provide sub-nm structures.
History
DepositionSep 28, 2017-
Header (metadata) releaseOct 25, 2017-
Map releaseOct 25, 2017-
UpdateDec 6, 2017-
Current statusDec 6, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3887.png

Downloads & links

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Map

FileDownload / File: emd_3887.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcrB in SMA polymer. Map filtered by local resolution in RELION 2.1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 128 pix.
= 272.64 Å		2.13 Å/pix.
x 128 pix.
= 272.64 Å		2.13 Å/pix.
x 128 pix.
= 272.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.13874209 - 0.28629002
Average (Standard dev.)0.0017829668 (±0.01858561)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 272.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.132.132.13
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z272.640272.640272.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1390.2860.002

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Supplemental data

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Sample components

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Entire : Escherichia coli multidrug efflux transporter AcrB in a SMALP platform

EntireName: Escherichia coli multidrug efflux transporter AcrB in a SMALP platform
Components
  • Complex: Escherichia coli multidrug efflux transporter AcrB in a SMALP platform

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Supramolecule #1: Escherichia coli multidrug efflux transporter AcrB in a SMALP platform

SupramoleculeName: Escherichia coli multidrug efflux transporter AcrB in a SMALP platform
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: C43(DE3)
Molecular weightTheoretical: 340 KDa

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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

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 70.0 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

Startup modelType of model: OTHER / Details: Low-pass filtered EM map
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26480
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER / Details: RELION auto-refinement

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