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- EMDB-19185: BmrA E504-100uMATPMg-IF -

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Basic information

Entry
Database: EMDB / ID: EMD-19185
TitleBmrA E504-100uMATPMg-IF
Map data
Sample
  • Complex: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
    • Protein or peptide: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
KeywordsBmrA / multidrug transporter / drug resistance / ABC transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


ATPase-coupled lipid transmembrane transporter activity / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type transporter activity / transmembrane transport / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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. ...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
Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsGobet A / Zarkadas E / Schoehn G / Falson P / Chaptal V
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0023-01 France
CitationJournal: Nat Commun / Year: 2025
Title: Rhodamine6G and Hœchst33342 narrow BmrA conformational spectrum for a more efficient use of ATP.
Authors: A Gobet / L Moissonnier / E Zarkadas / S Magnard / E Bettler / J Martin / R Terreux / G Schoehn / C Orelle / J M Jault / P Falson / V Chaptal /
Abstract: Multidrug ABC transporters harness the energy of ATP binding and hydrolysis to translocate substrates out of the cell and detoxify them. While this involves a well-accepted alternating access ...Multidrug ABC transporters harness the energy of ATP binding and hydrolysis to translocate substrates out of the cell and detoxify them. While this involves a well-accepted alternating access mechanism, molecular details of this interplay are still elusive. Rhodamine6G binding on a catalytic inactive mutant of the homodimeric multidrug ABC transporter BmrA triggers a cooperative binding of ATP on the two identical nucleotide-binding-sites, otherwise michaelian. Here, we investigate this asymmetric behavior via a structural-enzymology approach, solving cryoEM structures of BmrA at defined ATP ratios, highlighting the plasticity of BmrA as it undergoes the transition from inward to outward facing conformations. Analysis of continuous heterogeneity within cryoEM data and structural dynamics, reveals that Rhodamine6G narrows the conformational spectrum explored by the nucleotide-binding domains. We observe the same behavior for the other drug Hœchst33342. Following on these findings, the effect of drug-binding showed an ATPase stimulation and a maximal transport activity of the wild-type protein at the concentration-range where the cooperative transition occurs. Altogether, these findings provide a description of the influence of drug binding on the ATP-binding sites through a change in conformational dynamics.
History
DepositionDec 18, 2023-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19185.png

Downloads & links

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Map

FileDownload / File: emd_19185.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.)X (Row.)Y (Col.)
1.15 Å/pix.
x 200 pix.
= 229. Å		1.15 Å/pix.
x 200 pix.
= 229. Å		1.15 Å/pix.
x 200 pix.
= 229. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.218
Minimum - Maximum-0.51079035 - 0.83128697
Average (Standard dev.)0.002118521 (±0.027846662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 229.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_19185_additional_1.map
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Half map: #1

Fileemd_19185_half_map_1.map
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Half map: #2

Fileemd_19185_half_map_2.map
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Sample components

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Entire : Multidrug resistance ABC transporter ATP-binding/permease protein BmrA

EntireName: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
Components
  • Complex: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
    • Protein or peptide: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA

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Supramolecule #1: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA

SupramoleculeName: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Apo form, mutant E504A
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA

MacromoleculeName: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 65.747141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSSHHHHHH MPTKKQKSKS KLKPFFALVR RTNPSYGKLA FALALSVVTT LVSLLIPLLT KQLVDGFSMS NLSGTQIGLI ALVFFVQAG LSAYATYALN YNGQKIISGL RELLWKKLIK LPVSYFDTNA SGETVSRVTN DTMVVKELIT THISGFITGI I SVIGSLTI ...String:
MSSSHHHHHH MPTKKQKSKS KLKPFFALVR RTNPSYGKLA FALALSVVTT LVSLLIPLLT KQLVDGFSMS NLSGTQIGLI ALVFFVQAG LSAYATYALN YNGQKIISGL RELLWKKLIK LPVSYFDTNA SGETVSRVTN DTMVVKELIT THISGFITGI I SVIGSLTI LFIMNWKLTL LVLVVVPLAA LILVPIGRKM FSISRETQDE TARFTGLLNQ ILPEIRLVKA SNAEDVEYGR GK MGISSLF KLGVREAKVQ SLVGPLISLV LMAALVAVIG YGGMQVSSGE LTAGALVAFI LYLFQIIMPM GQITTFFTQL QKS IGATER MIEILAEEEE DTVTGKQIEN AHLPIQLDRV SFGYKPDQLI LKEVSAVIEA GKVTAIVGPS GGGKTTLFKL LERF YSPTA GTIRLGDEPV DTYSLESWRE HIGYVSQESP LMSGTIRENI CYGLERDVTD AEIEKAAEMA YALNFIKELP NQFDT EVGE RGIMLSGGQR QRIAIARALL RNPSILMLDA ATSSLDSQSE KSVQQALEVL MEGRTTIVIA HRLSTVVDAD QLLFVE KGE ITGRGTHHEL MASHGLYRDF AEQQLKMNAD LENKAG

UniProtKB: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA

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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: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 3218 / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3787631
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: ab-initio cryosparc
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: NU refinement / Number images used: 418416
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6r81


Chain - Chain ID: AB / Chain - Residue range: 1-580 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ria:
BmrA E504-100uMATPMg-IF

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