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- EMDB-65138: Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessu... -

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Basic information

Entry
Database: EMDB / ID: EMD-65138
TitleCryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)
Map data
Sample
  • Complex: Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit b-delta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHydrolase / ATP synthase / membrane protein / mycobacterium abscessus / mycobacterial / nontuberculous mycobacteria
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit ...ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit b / ATP synthase subunit b-delta / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesMycobacteroides abscessus subsp. abscessus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 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_65138.png

Downloads & links

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Map

FileDownload / File: emd_65138.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.76 Å
Density
Contour LevelBy AUTHOR: 0.072
Minimum - Maximum-0.33729586 - 0.80150187
Average (Standard dev.)0.00015238303 (±0.019937763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 516.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65138_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_65138_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_65138_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessu...

EntireName: Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)
Components
  • Complex: Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit b-delta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessu...

SupramoleculeName: Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Molecular weightTheoretical: 58.915211 KDa
Recombinant expressionOrganism: Mycobacteroides abscessus subsp. abscessus (bacteria)
SequenceString: MTELTISSAD ISGAIEQYVA TFSADPTREE IGIVSDAGDG IAHVEGLPSV MTQELLEFPG GVLGVALNLD ERSVGTVVLG DFQDIEEGQ QVKRTGEVLS VPVGDAFLGR VINPLGQPID GRGDIEAETR RALELQAPSV VQRQSVSEPL QTGIKAIDSQ T PIGRGQRQ ...String:
MTELTISSAD ISGAIEQYVA TFSADPTREE IGIVSDAGDG IAHVEGLPSV MTQELLEFPG GVLGVALNLD ERSVGTVVLG DFQDIEEGQ QVKRTGEVLS VPVGDAFLGR VINPLGQPID GRGDIEAETR RALELQAPSV VQRQSVSEPL QTGIKAIDSQ T PIGRGQRQ LIIGDRKTGK TAVCIDTILN QKQAWETGDP AQQVRCIYVA VGQKGSTVAA VRRTLDEAGA LEYTTIVAAP AS DAAGFKW LAPYTGSALG QHWMYQGKHV LIVFDDLTKQ AEAYRAISLL LRRPPGREAY PGDVFYLHSR LLERCAKLSD ELG AGSLTG LPIIETKAND ISAYIPTNVI SITDGQCFLQ TDLFNQGVRP AVNVGVSVSR VGGAAQIKAM KEVAGSLRLE LSQY RELEA FAAFASDLDA TSKAQLERGA RLVELLKQPQ NSPYPVEEQV VAIYLGTGGH LDSVPVEDVM RFEQEFLDHV RGSHA DILA DIRETKKFSE DTETKLTNAV NAFKKSFAAT DGSSVEVKGV AAEALDESAV GQETVQVRKP APKK

UniProtKB: ATP synthase subunit alpha

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Macromolecule #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Molecular weightTheoretical: 56.032949 KDa
Recombinant expressionOrganism: Mycobacteroides abscessus subsp. abscessus (bacteria)
SequenceString: MTAPTANKTA GRVVRVTGPV VDVEFPRDAV PPLFSALNAE ITYEAMAKTL TLEVAQHLGD NLVRTISMQP TDGLVRGVDV VSTGNTIAV PVGDGVKGHV FNALGNCLDE PGYGSDFEKW SIHRKPPAFD QLEPRTEMLE TGLKVVDLLT PYVRGGKIAL F GGAGVGKT ...String:
MTAPTANKTA GRVVRVTGPV VDVEFPRDAV PPLFSALNAE ITYEAMAKTL TLEVAQHLGD NLVRTISMQP TDGLVRGVDV VSTGNTIAV PVGDGVKGHV FNALGNCLDE PGYGSDFEKW SIHRKPPAFD QLEPRTEMLE TGLKVVDLLT PYVRGGKIAL F GGAGVGKT VLIQEMINRI ARNFGGTSVF AGVGERTREG NDLWVELADA NVLKDTALVF GQMDEPPGTR MRVALSALTM AE YFRDEQG QDVLLFIDNI FRFTQAGSEV STLLGRMPSA VGYQPTLADE MGELQERITS TRGRSITSMQ AVYVPADDYT DPA PATTFA HLDATTELSR AVFSKGIFPA VDPLASSSTI LLPSVVGEEH YRVAQEVIRI LQRYQDLQDI IAILGIDELS EEDK QLVGR ARRIERFLSQ NMMAAEQFTG QPGSTVPLKE TIEAFDKLTK GEFDHLPEQA FFLIGGLDDL AKKAESLGAK LGLSG QPPR SPSSGSSGGG GENLYFQDYK DDDDKHHHHH H

UniProtKB: ATP synthase subunit beta

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Macromolecule #3: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Molecular weightTheoretical: 33.189648 KDa
Recombinant expressionOrganism: Mycobacteroides abscessus subsp. abscessus (bacteria)
SequenceString: MGAQIRELRR RIKSAGAIKK ITKAQELIAT SRIAKAQARV VAARPYATEI TNVLTALADD AALDHPLLVE RPEPKRAGVL IVSSDRGLC GGYNANVLRV AEELYALLRE QGKTPVVYVV GRKALNYYSF RNRKVTEAWT GFSERPEYAS AQKIADTLVE A FLAGADDE ...String:
MGAQIRELRR RIKSAGAIKK ITKAQELIAT SRIAKAQARV VAARPYATEI TNVLTALADD AALDHPLLVE RPEPKRAGVL IVSSDRGLC GGYNANVLRV AEELYALLRE QGKTPVVYVV GRKALNYYSF RNRKVTEAWT GFSERPEYAS AQKIADTLVE A FLAGADDE GDDPGLDGIL GVDELHIVYT EFKSMLTQAA VAKRIAPMEV EYVGEAAGPT TQYSFEPDAT TLFGALLPRY LA TRVYAAL LEAAASESAS RRRAMKAATD NADELIKGLT LEANGARQAQ ITQEISEIVG GVNALADAAG H

UniProtKB: ATP synthase gamma chain

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Macromolecule #4: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Molecular weightTheoretical: 13.074608 KDa
Recombinant expressionOrganism: Mycobacteroides abscessus subsp. abscessus (bacteria)
SequenceString:
MSEIDVEIVA VEREIWSGKA TFVFTRTTSG EIGILPHHIP LVAQLVDDAA VKIEREGSDD LWWAIDGGFL SITDTKVSIL AESAQARAD IDEAKAKTDS GSEDPRVAAQ GRARLRALGQ TV

UniProtKB: ATP synthase epsilon chain

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Macromolecule #5: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Molecular weightTheoretical: 18.54375 KDa
Recombinant expressionOrganism: Mycobacteroides abscessus subsp. abscessus (bacteria)
SequenceString:
MGELHSVASA VTAVAAEAAE EGGKQNNFLI PNGTFFVVLA IFLIVLAVIG TFVVPPIQKV LKAREDMVTK TAEDNRNAAE QFTAAEADY KDELAKARGA ATAVRDEARA EGRGILEDMR QRANAEATAV TETAAAELAR QGEVTAGELA TNVDSLSRTL A ERVLGVSL SEPANAGRG

UniProtKB: ATP synthase subunit b

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Macromolecule #6: ATP synthase subunit b-delta

MacromoleculeName: ATP synthase subunit b-delta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus subsp. abscessus (bacteria)
Molecular weightTheoretical: 47.69598 KDa
Recombinant expressionOrganism: Mycobacteroides abscessus subsp. abscessus (bacteria)
SequenceString: MSTFIGQLIG FAVIVFLVVK YVVPPVRTLM AKQQDAVRQQ LADSKTAADK LVEAEGAHAK AIEDAKADAA QIAEEAKADA VQISKQLRE QADAEVERIK VHGQEQIVLQ RQQLIRQLRG DLGAESVRRA GDLVRSHVAD PSAQSATVDR FLDELSQMAG S VGAAKRPV ...String:
MSTFIGQLIG FAVIVFLVVK YVVPPVRTLM AKQQDAVRQQ LADSKTAADK LVEAEGAHAK AIEDAKADAA QIAEEAKADA VQISKQLRE QADAEVERIK VHGQEQIVLQ RQQLIRQLRG DLGAESVRRA GDLVRSHVAD PSAQSATVDR FLDELSQMAG S VGAAKRPV PGGYSGMHAA SRESLAAQVS TFRETAASLD SSALSALAED IAAVAELLIS ELVLRKHLSE PVDASENEAK LT LVNSLLG NKIGAPALAI VRSAVTARWS ASSDLITSLE YIARLALLER AERDGQIEDV EDQLFRVSRV LDAEPQLATL LSD STAPAQ GRVALLTNVL GGRANEVTTA LLAQTVRLLY SVRAEVAVLD VAELAVARRD ESVAHVKAAA PITDAQRTRL AQVL GQIYG RTIAVQLDVD PELLGGLVVN IGDEEIDGSL STRLSAAALH LPN

UniProtKB: ATP synthase subunit b-delta

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, 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

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) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 45839
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)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

mlw0

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

mlw0

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

mlw0

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

mlw2

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

mlw2

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

mlw2

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

mlw1

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

mlw3

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

mlv8

chain_id: b, source_name: Other, initial_model_type: in silico modelPhyre2.2

mlv9

chain_id: d, source_name: Other, initial_model_type: in silico modelPhyre2.2
Output model

PDB-9vkp:
Cryo-EM structure of F-ATP synthase from Mycobacteroides abscessus (Rotational State 1)

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