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- EMDB-53152: ATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in LMNG -

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Basic information

Entry
Database: EMDB / ID: EMD-53152
TitleATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in LMNG
Map dataCryo-EM map of the ATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in LMNG at 3.4 A resolution. Map was sharpened with a b factor of 104 A2
Sample
  • Complex: Wzm-Wzt
    • Protein or peptide: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
    • Protein or peptide: Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsABC transporter Type V ABC transporter Arabinogalactan precursor Lipid-linked galactan exporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


teichoic-acid-transporting ATPase / lipopolysaccharide transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ABC transporter, teichoic acids export TagH-like / : / ABC-2 type transporter / ABC-2 type transporter / 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
Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE / Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsGaraeva AA / Fabianova V / Savkova K / Huszar S / Xue X / Lowary TL / Mikusova K / Seeger MA
Funding supportEuropean Union, Switzerland, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)772190European Union
Swiss National Science FoundationPP00P3_170625 Switzerland
European Union (EU)NextGenerationEU, Recovery and Resilience Plan for Slovakia, project No. 09I01-03-V03- 00001European Union
University of ZurichFK-21-041 Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of lipid-linked galactan export by the mycobacterial ABC transporter Wzm-Wzt.
Authors: Alisa A Garaeva / Viktória Fabianová / Karin Savková / Stanislav Huszár / Xiaochao Xue / Todd L Lowary / Katarína Mikušová / Markus A Seeger /
Abstract: Mycobacteria, including Mycobacterium tuberculosis, possess a unique cell envelope containing arabinogalactan, a heteropolysaccharide critical for cell wall integrity and target of several ...Mycobacteria, including Mycobacterium tuberculosis, possess a unique cell envelope containing arabinogalactan, a heteropolysaccharide critical for cell wall integrity and target of several tuberculosis drugs. The cytosolic precursor of arabinogalactan, lipid-linked galactan (LLG), is translocated across the plasma membrane by the essential ABC transporter Wzm-Wzt through a molecular mechanism that is poorly understood. Here, we present a series of cryo-EM structures of Wzm-Wzt from Mycobacterium abscessus, representing different conformations of the transport cycle. Conserved residues lining the proposed LLG translocation pathway were investigated by three orthologous functional assays, revealing that the cytosolic gate helix (GH) plays a key functional role in polysaccharide transport. Our data suggests that the hydrophobic polyprenyl-moiety is translocated first, followed by the galactan-polysaccharide, which requires Wzm-Wzt to open a continuous channel through which the sugar chain is ratcheted at the expense of ATP hydrolysis. Our results provide a rational basis for the development of drugs that inhibit mycobacterial cell wall biosynthesis.
History
DepositionMar 17, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53152.png

Downloads & links

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Map

FileDownload / File: emd_53152.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the ATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in LMNG at 3.4 A resolution. Map was sharpened with a b factor of 104 A2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.253
Minimum - Maximum-1.0767086 - 1.5617023
Average (Standard dev.)0.0011028389 (±0.036971025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53152_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map A used for post processing step and...

Fileemd_53152_half_map_1.map
Annotationhalf-map A used for post processing step and FSC resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map B used for post processing step and...

Fileemd_53152_half_map_2.map
Annotationhalf-map B used for post processing step and FSC resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wzm-Wzt

EntireName: Wzm-Wzt
Components
  • Complex: Wzm-Wzt
    • Protein or peptide: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
    • Protein or peptide: Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Wzm-Wzt

SupramoleculeName: Wzm-Wzt / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacteroides abscessus (bacteria)

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Macromolecule #1: Probable O-antigen/lipopolysaccharide transport integral membrane...

MacromoleculeName: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
type: protein_or_peptide / ID: 1 / Details: MGSSHHHHHHSQ - expression tag / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 35.249207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQMSSSAGLT SQRPGSKEND MANELIELSS DSRTFKRAWR DLSEGFEHRQ LWLQLGWQDI KQRYRRSVLG PFWITIATG STALAMGILY SQLFKLPLAE HLPYVTIGLI VWNLFNAAIL EGSDVFVANE GLIKQLPTPL SVHVYRLVWR Q LLLFAHNI ...String:
MGSSHHHHHH SQMSSSAGLT SQRPGSKEND MANELIELSS DSRTFKRAWR DLSEGFEHRQ LWLQLGWQDI KQRYRRSVLG PFWITIATG STALAMGILY SQLFKLPLAE HLPYVTIGLI VWNLFNAAIL EGSDVFVANE GLIKQLPTPL SVHVYRLVWR Q LLLFAHNI IIFLIVVAVY TPHWHFTDLS FIPALVLITL NCLWVSLVFG VLATRYRDIS PLLGSLVQLL FFMTPIIWNE NM LNQRVGK LATVVQLNPF VHFLAIIRDP LLGLDQQLHH WIIALSITVV GWIVAIVVMR QYRARVPYWV

UniProtKB: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD

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Macromolecule #2: Probable o-antigen/lipopolysaccharide transport ATP-binding prote...

MacromoleculeName: Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: teichoic-acid-transporting ATPase
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 28.76401 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVSIQTHQAW VEFPIFDAKS RSLKKAFLGK AGGAIGRNES NVVVIEALRD ITLSLKEGDR VGLVGHNGAG KSTLLRLLSG IYEPTRGSS YIKGRVAPVF DLGVGMDPEI SGYENIIIRG MFLGQTRKQM QAKVDEIADF TELGEYLSMP LRTYSTGMRV R LAMGVVTS ...String:
MVSIQTHQAW VEFPIFDAKS RSLKKAFLGK AGGAIGRNES NVVVIEALRD ITLSLKEGDR VGLVGHNGAG KSTLLRLLSG IYEPTRGSS YIKGRVAPVF DLGVGMDPEI SGYENIIIRG MFLGQTRKQM QAKVDEIADF TELGEYLSMP LRTYSTGMRV R LAMGVVTS IDPEILLLDE GIGAVDAEFM KKARIRLQQL VERSGMLVFA SHSNEFLARL CNTAMWIDHG TIKMSGGIED VV RAYEGDE AGDHVAQILA EDAHDG

UniProtKB: Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

Concentration2 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl pH 8.0, 300 mM NaCl, 0.002% LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 90.0 K / Max: 105.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 8556 / Average exposure time: 1.3 sec. / Average electron dose: 64.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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: 4453645
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 40784
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9qh1:
ATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in LMNG

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