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- EMDB-19130: BmrA E504-R6G-25uMATP-Mg -

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Basic information

Entry
Database: EMDB / ID: EMD-19130
TitleBmrA E504-R6G-25uMATP-Mg
Map datasharpenned map
Sample
  • Complex: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
    • Protein or peptide: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
  • Ligand: RHODAMINE 6G
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: 3.9 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: To Be Published
Title: BmrA E504-R6G-25uMATPMg
Authors: Gobet A / Zarkadas E / Schoehn G / Falson P / Chaptal V
History
DepositionDec 13, 2023-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19130.png

Downloads & links

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Map

FileDownload / File: emd_19130.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpenned map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 269.312 Å		1.05 Å/pix.
x 256 pix.
= 269.312 Å		1.05 Å/pix.
x 256 pix.
= 269.312 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.195
Minimum - Maximum-0.6200111 - 0.9720142
Average (Standard dev.)0.00099104 (±0.025830634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 269.312 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: non-sharpened map

Fileemd_19130_additional_1.map
Annotationnon-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19130_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19130_half_map_2.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 : 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
  • Ligand: RHODAMINE 6G

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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: #1 / 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
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
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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Macromolecule #2: RHODAMINE 6G

MacromoleculeName: RHODAMINE 6G / type: ligand / ID: 2 / Number of copies: 2 / Formula: RHQ
Molecular weightTheoretical: 443.557 Da
Chemical component information

ChemComp-R6G:
RHODAMINE 6G

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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: C-flat-1.2/1.3 / Material: GOLD / 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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5418 / Average exposure time: 0.969 sec. / Average electron dose: 38.79 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 130000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4864322
Startup modelType of model: NONE / Details: ab-initio cryosparc
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: NU refinement / Number images used: 150715
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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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-8rg7:
BmrA E504-R6G-25uMATP-Mg

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