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- PDB-9qhx: ATP-bound E178Q Wzm-Wzt from Mycobacterium abscessus in nanodiscs -

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Basic information

Entry
Database: PDB / ID: 9qhx
TitleATP-bound E178Q Wzm-Wzt from Mycobacterium abscessus in nanodiscs
Components
  • ABC transporter ATP-binding protein
  • ABC transporter permease
KeywordsMEMBRANE PROTEIN / ABC transporter Type V ABC transporter Arabinogalactan precursor Lipid-linked galactan exporter
Function / homology
Function and homology information


teichoic-acid-transporting ATPase / 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
ADENOSINE-5'-TRIPHOSPHATE / ABC transporter ATP-binding protein / ABC transporter permease
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsGaraeva, A.A. / Fabianova, V. / Savkova, K. / Huszar, S. / Xue, X. / Lowary, T.L. / Mikusova, K. / Seeger, M.A.
Funding supportEuropean Union, Switzerland, 4items
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 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter permease
B: ABC transporter permease
C: ABC transporter ATP-binding protein
D: ABC transporter ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4678
Polymers127,4044
Non-polymers1,0634
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ABC transporter permease


Mass: 35249.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSQ - expression tag / Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: D2E76_07265 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ABD7HS64
#2: Protein ABC transporter ATP-binding protein / Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE


Mass: 28452.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: tagH, D2E76_07275, ERS075527_00637, ERS075579_04253 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U0YYE2, teichoic-acid-transporting ATPase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Wzm-Wzt / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20 mM Tris-HCl pH 7.5, 150 mM NaCl
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: at 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 105 K / Temperature (min): 90 K
Image recordingAverage exposure time: 1.3 sec. / Electron dose: 66.46 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7425
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3324761
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208854 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 9QHW

9qhw


Accession code: 9QHW / Source name: PDB / Type: experimental model

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