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- EMDB-7609: Single particles Cryo-EM structure of AcrB D407A associated with ... -

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Basic information

Entry
Database: EMDB / ID: 7609
TitleSingle particles Cryo-EM structure of AcrB D407A associated with lipid bilayer at 3.0 Angstrom
Map dataprimary map
SampleLipid bilayer in AcrB:
Multidrug efflux pump subunit AcrB / (ligand) x 2
Function / homologyAcriflavin resistance protein / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / drug:proton antiporter activity / efflux pump complex / efflux transmembrane transporter activity / drug transmembrane transport / drug transmembrane transporter activity / response to drug ...Acriflavin resistance protein / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / drug:proton antiporter activity / efflux pump complex / efflux transmembrane transporter activity / drug transmembrane transport / drug transmembrane transporter activity / response to drug / integral component of plasma membrane / membrane / identical protein binding / plasma membrane / Multidrug efflux pump subunit AcrB
Function and homology information
SourceEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / 3 Å resolution
AuthorsQiu W / Fu Z / Guo Y
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure and activity of lipid bilayer within a membrane-protein transporter.
Authors: Weihua Qiu / Ziao Fu / Guoyan G Xu / Robert A Grassucci / Yan Zhang / Joachim Frank / Wayne A Hendrickson / Youzhong Guo
Validation ReportPDB-ID: 6csx

SummaryFull reportAbout validation report
DateDeposition: Mar 21, 2018 / Header (metadata) release: Mar 28, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6csx
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7609.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
0.85 Å/pix.
= 273.28 Å
320 pix
0.85 Å/pix.
= 273.28 Å
320 pix
0.85 Å/pix.
= 273.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.854 Å
Density
Contour Level:0.025 (by author), 0.035 (movie #1):
Minimum - Maximum-0.08175247 - 0.1653417
Average (Standard dev.)0.000293929 (0.0077259387)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin0.00.00.0
Limit319.0319.0319.0
Spacing320320320
CellA=B=C: 273.28 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8540.8540.854
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z273.280273.280273.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0820.1650.000

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Supplemental data

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Sample components

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Entire Lipid bilayer in AcrB

EntireName: Lipid bilayer in AcrB / Number of components: 4

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Component #1: protein, Lipid bilayer in AcrB

ProteinName: Lipid bilayer in AcrB / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Multidrug efflux pump subunit AcrB

ProteinName: Multidrug efflux pump subunit AcrB
Details: AcrB, lipid bilayerAcriflavine resistance protein family
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 114.692289 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: ligand, PHOSPHATIDYLETHANOLAMINE

LigandName: PHOSPHATIDYLETHANOLAMINE / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 0.734039 kDa

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Component #4: ligand, DODECANE

LigandName: DODECANE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.170335 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/ml / pH: 7.8
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 41190
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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