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- EMDB-65141: Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides a... -

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Basic information

Entry
Database: EMDB / ID: EMD-65141
TitleCryo-EM structure of F-ATP synthase c-ring from Mycobacteroides abscessus (Backbone)
Map data
Sample
  • Complex: Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides abscessus (Backbone)
    • Protein or peptide: ATP 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.61 Å
AuthorsFong TC / Saw W-G / Mathiyazakan V / Wong CF / Grueber G
Funding support Singapore, 1 items
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, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65141.png

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Map

FileDownload / File: emd_65141.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 400 pix.
= 304. Å		0.76 Å/pix.
x 400 pix.
= 304. Å		0.76 Å/pix.
x 400 pix.
= 304. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.16385327 - 0.30931708
Average (Standard dev.)0.00010496718 (±0.00472529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65141_msk_1.map
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Half map: #1

Fileemd_65141_half_map_1.map
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Half map: #2

Fileemd_65141_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides a...

EntireName: Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides abscessus (Backbone)
Components
  • Complex: Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides abscessus (Backbone)
    • Protein or peptide: ATP synthase subunit c

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Supramolecule #1: Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides a...

SupramoleculeName: Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides abscessus (Backbone)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)

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Macromolecule #1: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Molecular weightTheoretical: 8.158476 KDa
Recombinant expressionOrganism: Mycobacteroides abscessus subsp. abscessus (bacteria)
SequenceString:
MADPTIVAGA LIGGGLIMAG GAIGAGIGDG IAGNALISGV ARQPEAQGRL FTPFFITVGL VEAAYFINLA FMALFVFATP GAS

UniProtKB: ATP synthase subunit c

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 3 / Average exposure time: 3.25 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 46774
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

mlv7

chain_id: L, source_name: AlphaFold, initial_model_type: in silico model

mlv7

chain_id: M, source_name: AlphaFold, initial_model_type: in silico model

mlv7

chain_id: N, source_name: AlphaFold, initial_model_type: in silico model

mlv7

chain_id: O, source_name: AlphaFold, initial_model_type: in silico model

mlv7

chain_id: P, source_name: AlphaFold, initial_model_type: in silico model

mlv7

chain_id: Q, source_name: AlphaFold, initial_model_type: in silico model

mlv7

chain_id: R, source_name: AlphaFold, initial_model_type: in silico model

mlv7

chain_id: S, source_name: AlphaFold, initial_model_type: in silico model

mlv7

chain_id: T, source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-9vks:
Cryo-EM structure of F-ATP synthase c-ring from Mycobacteroides abscessus (Backbone)

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