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- EMDB-23803: A. baumannii MsbA in complex with TBT1 decoupler -

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Basic information

Entry
Database: EMDB / ID: EMD-23803
TitleA. baumannii MsbA in complex with TBT1 decoupler
Map dataA. baumannii MsbA in complex with TBT1 decoupler
Sample
  • Complex: A. baumannii MsbA in complex with TBT1 decoupler
    • Protein or peptide: ATP-dependent lipid A-core flippase
  • Ligand: 2-(4-chlorobenzamido)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylic acid
KeywordsMembrane protein
Function / homology
Function and homology information


ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ABC transporter, lipid A-core flippase, MsbA / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...ABC transporter, lipid A-core flippase, MsbA / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Lipid A export permease/ATP-binding protein MsbA
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsThelot F / Liao M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2021
Title: Distinct allosteric mechanisms of first-generation MsbA inhibitors.
Authors: François A Thélot / Wenyi Zhang / KangKang Song / Chen Xu / Jing Huang / Maofu Liao /
Abstract: ATP-binding cassette (ABC) transporters couple adenosine 5′-triphosphate (ATP) hydrolysis to substrate transport across biological membranes. Although many are promising drug targets, their ...ATP-binding cassette (ABC) transporters couple adenosine 5′-triphosphate (ATP) hydrolysis to substrate transport across biological membranes. Although many are promising drug targets, their mechanisms of modulation by small-molecule inhibitors remain largely unknown. Two first-generation inhibitors of the MsbA transporter, tetrahydrobenzothiophene 1 (TBT1) and G247, induce opposite effects on ATP hydrolysis. Using single-particle cryo–electron microscopy and functional assays, we show that TBT1 and G247 bind adjacent yet separate pockets in the MsbA transmembrane domains. Two TBT1 molecules asymmetrically occupy the substrate-binding site, which leads to a collapsed inward-facing conformation with decreased distance between the nucleotide-binding domains (NBDs). By contrast, two G247 molecules symmetrically increase NBD distance in a wide inward-open state of MsbA. The divergent mechanisms of action of these MsbA inhibitors provide important insights into ABC transporter pharmacology.
History
DepositionApr 7, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7met
  • Surface level: 2.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23803.png

Downloads & links

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Map

FileDownload / File: emd_23803.map.gz / Format: CCP4 / Size: 6.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA. baumannii MsbA in complex with TBT1 decoupler
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 109 pix.
= 115.54 Å		1.06 Å/pix.
x 107 pix.
= 113.42 Å		1.06 Å/pix.
x 154 pix.
= 163.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.03 / Movie #1: 2.03
Minimum - Maximum-14.693777000000001 - 20.274076000000001
Average (Standard dev.)0.000000000025373 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin413843
Dimensions107154109
Spacing109107154
CellA: 115.53999 Å / B: 113.41999 Å / C: 163.23999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z109107154
origin x/y/z0.0000.0000.000
length x/y/z115.540113.420163.240
α/β/γ90.00090.00090.000
start NX/NY/NZ434138
NX/NY/NZ109107154
MAP C/R/S321
start NC/NR/NS384143
NC/NR/NS154107109
D min/max/mean-14.69420.2740.000

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Supplemental data

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Additional map: unfiltered, unsharpened map

Fileemd_23803_additional_1.map
Annotationunfiltered, unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A. baumannii MsbA in complex with TBT1 decoupler

EntireName: A. baumannii MsbA in complex with TBT1 decoupler
Components
  • Complex: A. baumannii MsbA in complex with TBT1 decoupler
    • Protein or peptide: ATP-dependent lipid A-core flippase
  • Ligand: 2-(4-chlorobenzamido)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylic acid

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Supramolecule #1: A. baumannii MsbA in complex with TBT1 decoupler

SupramoleculeName: A. baumannii MsbA in complex with TBT1 decoupler / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: ATP-dependent lipid A-core flippase

MacromoleculeName: ATP-dependent lipid A-core flippase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: ABC-type lipid A-core oligosaccharide transporter
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 67.758688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MMHHHHHHHH GGVNQDFKVY LRLISYLKPY WGVALLVLIG FGMNSATEVS VAKLIKFIID AIQNASRAD LDWFPLLIIL LVFFRGLGLF MGGYYTAVIS RSLVFSIRQE VYAKLLRLPA QYYLDNSSGH ITAKIMYNVE Q LTAASSES ...String:
MGSSHHHHHH SSGLVPRGSH MMHHHHHHHH GGVNQDFKVY LRLISYLKPY WGVALLVLIG FGMNSATEVS VAKLIKFIID AIQNASRAD LDWFPLLIIL LVFFRGLGLF MGGYYTAVIS RSLVFSIRQE VYAKLLRLPA QYYLDNSSGH ITAKIMYNVE Q LTAASSES LKTIVRDGMI TLGLLGYLFY TNWRLTICIM VFLPIIGILV RKASKRMRKL SMQVQDTMGD VNHVVQESIN GN AVVKSFA GEESEQERFY KSSEENLKRG LKMVIVQNLN SPVVQVVMAC AMALIVWLAL RPQILGNTTA GEFVAYITAA GLL SKPVKN LTDVNEKLQR GLAAAHSVFE LLDLPEEQNS GELKPQLQGA IRFDHVVLNY ADGTQAIKDF SLDIRPGETV ALVG RSGAG KTSLVNMLVR FQEVSSGQIY LDDLPIRDIE LSSLRTQIAM VNQQVVLFNR TVRENIAYGQ LHNASDEDVI AAAKA AYAH DFIMNLPNGY DTVLGAQGLN LSGGQRQRIA IARAILKNAP ILILDEATSA LDNESEHFIQ QAFDEAMQDR TTIVIA HRL STIENADRIV VMDRGQIVEQ GTHQELLAKH GAYYQLHQRN FEDH

UniProtKB: Lipid A export permease/ATP-binding protein MsbA

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Macromolecule #2: 2-(4-chlorobenzamido)-4,5,6,7-tetrahydro-1-benzothiophene-3-carbo...

MacromoleculeName: 2-(4-chlorobenzamido)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylic acid
type: ligand / ID: 2 / Number of copies: 2 / Formula: Z5G
Molecular weightTheoretical: 335.805 Da
Chemical component information

ChemComp-Z5G:
2-(4-chlorobenzamido)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylic acid

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67714
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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