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- EMDB-51938: Structure of BmrA T123C-S428C cross-linked form (apo state) -

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Basic information

Entry
Database: EMDB / ID: EMD-51938
TitleStructure of BmrA T123C-S428C cross-linked form (apo state)
Map data
Sample
  • Complex: Homodimeric ATP-Binding Cassette Transporter BmrA
    • Protein or peptide: Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
KeywordsABC transporter / drug efflux pump / antibiotic resistance / homodimer / membrane protein / 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: 4.26 Å
AuthorsHanssen E / Valimehr S / Di Cesare M / Kaplan E / Coureux P-D / Orelle C / Jault J-M
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0023 France
CitationJournal: To Be Published
Title: Structure of BmrA T123C-S428C cross-linked form (apo state)
Authors: Di Cesare M / Kaplan E / Hanssen E / Valimehr S / Coureux P-D / Orelle C / Jault J-M
History
DepositionOct 29, 2024-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51938.png

Downloads & links

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Map

FileDownload / File: emd_51938.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.11936825 - 0.50600785
Average (Standard dev.)0.00021185033 (±0.013806746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51938_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_51938_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_51938_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51938_half_map_2.map
Projections & Slices
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Sample components

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Entire : Homodimeric ATP-Binding Cassette Transporter BmrA

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

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Supramolecule #1: Homodimeric ATP-Binding Cassette Transporter BmrA

SupramoleculeName: Homodimeric ATP-Binding Cassette Transporter BmrA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (bacteria)

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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: 66.326875 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPTKKQKSKS KLKPFFALVR RTNPSYGKLA FALALSVVTT LVSLLIPLLT KQLVDGFSMS NLSGTQIGLI ALVFFVQAGL SAYATYALN YNGQKIISGL RELLWKKLIK LPVSYFDTNA SGECVSRVTN DTMVVKELIT THISGFITGI ISVIGSLTIL F IMNWKLTL ...String:
MPTKKQKSKS KLKPFFALVR RTNPSYGKLA FALALSVVTT LVSLLIPLLT KQLVDGFSMS NLSGTQIGLI ALVFFVQAGL SAYATYALN YNGQKIISGL RELLWKKLIK LPVSYFDTNA SGECVSRVTN DTMVVKELIT THISGFITGI ISVIGSLTIL F IMNWKLTL LVLVVVPLAA LILVPIGRKM FSISRETQDE TARFTGLLNQ ILPEIRLVKA SNAEDVEYGR GKMGISSLFK LG VREAKVQ SLVGPLISLV LMAALVAVIG YGGMQVSSGE LTAGALVAFI LYLFQIIMPM GQITTFFTQL QKSIGATERM IEI LAEEEE DTVTGKQIEN AHLPIQLDRV SFGYKPDQLI LKEVSAVIEA GKVTAIVGPS GGGKTTLFKL LERFYSPTAG TIRL GDEPV DTYSLESWRE HIGYVSQESP LMCGTIRENI SYGLERDVTD AEIEKAAEMA YALNFIKELP NQFDTEVGER GIMLS GGQR QRIAIARALL RNPSILMLDE ATSSLDSQSE KSVQQALEVL MEGRTTIVIA HRLSTVVDAD QLLFVEKGEI TGRGTH HEL MASHGLYRDF AEQQLKMNAD LENKAGVDKL AAALEHHHHH H

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

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
50.0 mMNaClSodium chloride
0.035 %C24H46O11B-DDM
0.03 %C24H39NaO5Sodium cholate

Details: pH adjustment with sodium hydroxide
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10522608
CTF correctionSoftware - Name: cryoSPARC / Software - details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 777796
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8qoe


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial rigid-body fitting was done in Phenix using the TMD and NBD separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9h8o:
Structure of BmrA T123C-S428C cross-linked form (apo state)

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