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- PDB-9vks: Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides a... -

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Basic information

Entry
Database: PDB / ID: 9vks
TitleCryo-EM structure of F-ATP synthase c-ring from Mycobacteroides abscessus (Backbone)
ComponentsATP synthase subunit c
KeywordsHYDROLASE / ATP synthase / membrane protein / mycobacterium abscessus / mycobacterial / c-ring / nontuberculous mycobacteria
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase subunit c
Similarity search - Component
Biological speciesMycobacteroides abscessus subsp. abscessus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.61 Å
AuthorsFong, T.C. / Saw, W.-G. / Mathiyazakan, V. / Wong, C.F. / Grueber, G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-CRP27-2021-0002 Singapore
CitationJournal: Structure / Year: 2025
Title: The Mycobacterium abscessus F-ATP synthase structure reveals mechanistic elements enabling rational drug design to combat NTM lung disease.
Authors: Tuck Choy Fong / Wuan-Geok Saw / Vikneswaran Mathiyazakan / Chui Fann Wong / Gerhard Grüber /
Abstract: The increasing global incidence rate of nontuberculous mycobacteria pulmonary infections is an emerging public health crisis, with Mycobacterium abscessus (Mab) being one of the most virulent and ...The increasing global incidence rate of nontuberculous mycobacteria pulmonary infections is an emerging public health crisis, with Mycobacterium abscessus (Mab) being one of the most virulent and treatment-refractory of these pathogens. Mab exhibits extensive intrinsic and acquired drug resistance mechanisms that neutralize most antimicrobials against this pathogen, causing a clinical conundrum. As Mab relies on oxidative phosphorylation as its main energy source, its essential F-ATP synthase is a promising drug target but remains poorly understood due to a lack of host expression systems. Here, we present the expression, isolation, and structural characterization of Mab's F-ATP synthase. Cryo-EM reveals three nucleotide-driven rotational states at atomic resolution, highlighting key catalytic centers, a mycobacteria-specific α-subunit extension involved in the inhibition of ATP hydrolysis, energy transmission via the γε-stalk, and mechanochemical coupling by the δ-subunit. The structural blueprint allows precise target engagement and optimization of hits-to-leads and existing anti-Mab inhibitors targeting the engine.
History
DepositionJun 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 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

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit c
B: ATP synthase subunit c
C: ATP synthase subunit c
D: ATP synthase subunit c
E: ATP synthase subunit c
F: ATP synthase subunit c
G: ATP synthase subunit c
H: ATP synthase subunit c
I: ATP synthase subunit c


Theoretical massNumber of molelcules
Total (without water)73,4269
Polymers73,4269
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ATP synthase subunit c / ATP synthase F(0) sector subunit c / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 8158.476 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus subsp. abscessus (bacteria)
Gene: atpE, MAB_1448
Production host: Mycobacteroides abscessus subsp. abscessus (bacteria)
References: UniProt: B1MLV7
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: Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides abscessus (Backbone)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Source (recombinant)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: 165000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.25 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 3
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2EPU3.3.1image acquisition
4cryoSPARC4.6.0CTF correction
7UCSF ChimeraX1.8model fitting
8Coot0.9.8.95model fitting
10PHENIX1.21.2model refinement
11Coot0.9.8.95model refinement
12cryoSPARC4.6.0initial Euler assignment
13cryoSPARC4.6.0final Euler assignment
14cryoSPARC4.6.0classification
15cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46774 / Symmetry type: POINT
Atomic model building
ID 3D fitting-IDAccession codeChain-IDInitial refinement model-IDSource nameType
11B1MLV7L1AlphaFoldin silico model
21B1MLV7M1AlphaFoldin silico model
31B1MLV7N1AlphaFoldin silico model
41B1MLV7O1AlphaFoldin silico model
51B1MLV7P1AlphaFoldin silico model
61B1MLV7Q1AlphaFoldin silico model
71B1MLV7R1AlphaFoldin silico model
81B1MLV7S1AlphaFoldin silico model
91B1MLV7T1AlphaFoldin silico model
RefinementHighest resolution: 5.61 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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