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

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Basic information

Entry
Database: PDB / ID: 9qh1
TitleATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in LMNG
Components
  • Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
  • Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
KeywordsMEMBRANE PROTEIN / ABC transporter Type V ABC transporter Arabinogalactan precursor Lipid-linked galactan exporter
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
ADENOSINE-5'-TRIPHOSPHATE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 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: Garaeva, A.A. / Fabianova, V. / Savkova, K. / Huszar, S. / Xue, X. / Lowary, T.L. / Mikusova, K. / Seeger, M.A.
History
DepositionMar 17, 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
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
B: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
C: Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
D: Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0898
Polymers128,0264
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 Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD


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: MAB_0201c / Production host: Escherichia coli (E. coli) / References: UniProt: B1MEN7
#2: Protein Probable o-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE


Mass: 28764.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: tagH, SAMEA2070301_03522, SAMEA2070793_04484 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1N1NVQ2, 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-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl pH 8.0, 300 mM NaCl, 0.002% LMNG
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 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: 64.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8556
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: 4453645
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40784 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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