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- EMDB-4749: Multidrug resistance transporter BmrA mutant E504A bound with ATP... -

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Basic information

Entry
Database: EMDB / ID: EMD-4749
TitleMultidrug resistance transporter BmrA mutant E504A bound with ATP and Mg solved by Cryo-EM
Map data
SampleMultidrug resistance transporter from Bacillus subtilis bound with ATP and Mg.
  • Lipid A export ATP-binding/permease protein MsbA
  • (ligand) x 2
Function / homology
Function and homology information


Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / ATPase-coupled transmembrane transporter activity / transmembrane transport / ATPase activity / response to antibiotic / integral component of membrane / ATP binding / plasma membrane
ABC transporter-like / Type I protein exporter / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain / AAA+ ATPase domain
Lipid A export ATP-binding/permease protein MsbA / Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWiseman B / Chaptal V / Zampieri V / Magnard S / Hogbom M / Falson P
Funding support France, Sweden, 3 items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0015-03 France
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Structure of the multidrug resistance transporter BmrA
Authors: Chaptal V / Zampieri V / Wiseman B / N'Guyen K / Magnard S / Kilburg A / Peuchmaur M / Martin J / Orelle C / Jault JM / Monticelli L / Hogbom M / Boumendjel A / Falson P
Validation ReportPDB-ID: 6r81

SummaryFull reportAbout validation report
History
DepositionMar 30, 2019-
Header (metadata) releaseMay 6, 2020-
Map releaseMay 6, 2020-
UpdateMay 6, 2020-
Current statusMay 6, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.33
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r81
  • Surface level: 0.33
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4749.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å
1.06 Å/pix.
x 200 pix.
= 212. Å
1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.33 / Movie #1: 0.33
Minimum - Maximum-28.452795 - 34.898476
Average (Standard dev.)-0.00000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.7651.4620.010

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Supplemental data

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Additional map: Sharpened map used to aid and improve model building in many areas.

Fileemd_4749_additional.map
AnnotationSharpened map used to aid and improve model building in many areas.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Multidrug resistance transporter from Bacillus subtilis bound wit...

EntireName: Multidrug resistance transporter from Bacillus subtilis bound with ATP and Mg.
Details: mutant E504A / Number of components: 4

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Component #1: protein, Multidrug resistance transporter from Bacillus subtilis ...

ProteinName: Multidrug resistance transporter from Bacillus subtilis bound with ATP and Mg.
Details: mutant E504A / Recombinant expression: No
SourceSpecies: Bacillus subtilis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET15b / Strain: C43, delta-AcrB

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Component #2: protein, Lipid A export ATP-binding/permease protein MsbA

ProteinName: Lipid A export ATP-binding/permease protein MsbA / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 65.747141 kDa
SourceSpecies: Bacillus subtilis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 3.5 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3477

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 128372
3D reconstructionSoftware: cryoSPARC / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL / Overall bvalue: 187
Output model

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