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- EMDB-50783: MsbA in UDM inward-facing wide (+) open -

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Basic information

Entry
Database: EMDB / ID: EMD-50783
TitleMsbA in UDM inward-facing wide (+) open
Map data
Sample
  • Complex: MsbA
    • Protein or peptide: ATP-dependent lipid A-core flippase
KeywordsABC transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type lipid A-core oligosaccharide transporter / ABC-type oligopeptide transporter activity / ATPase-coupled lipid transmembrane transporter activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Lipid A export ATP-binding/permease protein msbA family profile. / 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 ...Lipid A export ATP-binding/permease protein msbA family profile. / 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
ATP-dependent lipid A-core flippase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHoffmann L / Baier A / Jorde L / Kamel M / Schaefer J / Schnelle K / Scholz A / Shvarev D / Wong J / Parey K ...Hoffmann L / Baier A / Jorde L / Kamel M / Schaefer J / Schnelle K / Scholz A / Shvarev D / Wong J / Parey K / Januliene D / Moeller A
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 944 Germany
German Research Foundation (DFG)SFB 1557 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
CitationJournal: Structure / Year: 2025
Title: The ABC transporter MsbA in a dozen environments.
Authors: Lea Hoffmann / Anika Baier / Lara Jorde / Michael Kamel / Jan-Hannes Schäfer / Kilian Schnelle / Alischa Scholz / Dmitry Shvarev / Jaslyn E M M Wong / Kristian Parey / Dovile Januliene / Arne Moeller /
Abstract: High-resolution structure determination of membrane proteins typically requires reconstitution into artificial membrane mimics. The choice of the specific membrane substitute can strongly affect the ...High-resolution structure determination of membrane proteins typically requires reconstitution into artificial membrane mimics. The choice of the specific membrane substitute can strongly affect the protein's specific activity, stability, and conformational spectrum, potentially leading to errors or misinterpretation during analysis. The bacterial ATP-binding cassette transporter MsbA is a prominent example of such environment-specific bias. Here, we present a systematic analysis of the conformational spectrum of MsbA, stabilized in a dozen environments, using cryoelectron microscopy (cryo-EM), and show pronounced feedback between the membrane mimetics and the transporter. Detergents generally favor wide inward-facing conformations while nanodiscs induce narrower conformations. Notably, only in three tested environments, MsbA samples the full movement of the nucleotide-binding domains, including narrow and wide conformations. We expect this study to serve as a blueprint for other membrane proteins, even where a structural reaction to the hydrophobic environment is not directly visible but still critical for the proteins' function.
History
DepositionJun 26, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50783.png

Downloads & links

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Map

FileDownload / File: emd_50783.map.gz / Format: CCP4 / Size: 231.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 393 pix.
= 267.24 Å		0.68 Å/pix.
x 393 pix.
= 267.24 Å		0.68 Å/pix.
x 393 pix.
= 267.24 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.12959605 - 0.32649887
Average (Standard dev.)0.0010579708 (±0.0091409385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions393393393
Spacing393393393
CellA=B=C: 267.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_50783_additional_1.map
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Half map: #1

Fileemd_50783_half_map_1.map
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Half map: #2

Fileemd_50783_half_map_2.map
Projections & Slices
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Sample components

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Entire : MsbA

EntireName: MsbA
Components
  • Complex: MsbA
    • Protein or peptide: ATP-dependent lipid A-core flippase

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Supramolecule #1: MsbA

SupramoleculeName: MsbA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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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: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.986891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TFRRLWPTIA PFKAGLIVAG VALILNAASD TFMLSLLKPL LDDGFGKTDR SVLVWMPLVV IGLMILRGIT SYVSSYCISW VSGKVVMTM RRRLFGHMMG MPVSFFDKQS TGTLLSRITY DSEQVASSSS GALITVVREG ASIIGLFIMM FYYSWQLSII L IVLAPIVS ...String:
TFRRLWPTIA PFKAGLIVAG VALILNAASD TFMLSLLKPL LDDGFGKTDR SVLVWMPLVV IGLMILRGIT SYVSSYCISW VSGKVVMTM RRRLFGHMMG MPVSFFDKQS TGTLLSRITY DSEQVASSSS GALITVVREG ASIIGLFIMM FYYSWQLSII L IVLAPIVS IAIRVVSKRF RNISKNMQNT MGQVTTSAEQ MLKGHKEVLI FGGQEVETKR FDKVSNRMRL QGMKMVSASS IS DPIIQLI ASLALAFVLY AASFPSVMDS LTAGTITVVF SSMIALMRPL KSLTNVNAQF QRGMAACQTL FTILDSEQEK DEG KRVIER ATGDVEFRNV TFTYPGRDVP ALRNINLKIP AGKTVALVGR SGSGKSTIAS LITRFYDIDE GEILMDGHDL REYT LASLR NQVALVSQNV HLFNDTVANN IAYARTEQYS REQIEEAARM AYAMDFINKM DNGLDTVIGE NGVLLSGGQR QRIAI ARAL LRDSPILILD EATSALDTES ERAIQAALDE LQKNRTSLVI AHRLSTIEKA DEIVVVEDGV IVERGTHNDL LEHRGV YAQ LHKMQF

UniProtKB: ATP-dependent lipid A-core flippase

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162890
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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