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- EMDB-36589: Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-36589
TitleCryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with TBAJ-587
Map data
Sample
  • Complex: Mycobacterium tuberculosis ATP synthase
    • Protein or peptide: x 4 types
  • Protein or peptide: x 4 types
  • Ligand: x 4 types
KeywordsATP synthase / Mycobacterium tuberculosis / cryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / : / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / peptidoglycan-based cell wall / ADP binding / hydrolase activity ...proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / : / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / peptidoglycan-based cell wall / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane / cytosol
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 A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site ...ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / 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, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / 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 c / ATP synthase subunit a / Multifunctional fusion protein / ATP synthase subunit beta / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase epsilon chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhang Y / Lai Y / Liu F / Rao Z / Gong H
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: Nature / Year: 2024
Title: Inhibition of M. tuberculosis and human ATP synthase by BDQ and TBAJ-587.
Authors: Yuying Zhang / Yuezheng Lai / Shan Zhou / Ting Ran / Yue Zhang / Ziqing Zhao / Ziyan Feng / Long Yu / Jinxu Xu / Kun Shi / Jianyun Wang / Yu Pang / Liang Li / Hongming Chen / Luke W Guddat / ...Authors: Yuying Zhang / Yuezheng Lai / Shan Zhou / Ting Ran / Yue Zhang / Ziqing Zhao / Ziyan Feng / Long Yu / Jinxu Xu / Kun Shi / Jianyun Wang / Yu Pang / Liang Li / Hongming Chen / Luke W Guddat / Yan Gao / Fengjiang Liu / Zihe Rao / Hongri Gong /
Abstract: Bedaquiline (BDQ), a first-in-class diarylquinoline anti-tuberculosis drug, and its analogue, TBAJ-587, prevent the growth and proliferation of Mycobacterium tuberculosis by inhibiting ATP synthase. ...Bedaquiline (BDQ), a first-in-class diarylquinoline anti-tuberculosis drug, and its analogue, TBAJ-587, prevent the growth and proliferation of Mycobacterium tuberculosis by inhibiting ATP synthase. However, BDQ also inhibits human ATP synthase. At present, how these compounds interact with either M. tuberculosis ATP synthase or human ATP synthase is unclear. Here we present cryogenic electron microscopy structures of M. tuberculosis ATP synthase with and without BDQ and TBAJ-587 bound, and human ATP synthase bound to BDQ. The two inhibitors interact with subunit a and the c-ring at the leading site, c-only sites and lagging site in M. tuberculosis ATP synthase, showing that BDQ and TBAJ-587 have similar modes of action. The quinolinyl and dimethylamino units of the compounds make extensive contacts with the protein. The structure of human ATP synthase in complex with BDQ reveals that the BDQ-binding site is similar to that observed for the leading site in M. tuberculosis ATP synthase, and that the quinolinyl unit also interacts extensively with the human enzyme. This study will improve researchers' understanding of the similarities and differences between human ATP synthase and M. tuberculosis ATP synthase in terms of the mode of BDQ binding, and will allow the rational design of novel diarylquinolines as anti-tuberculosis drugs.
History
DepositionJun 15, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36589.png

Downloads & links

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Map

FileDownload / File: emd_36589.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.6
Minimum - Maximum-27.483136999999999 - 41.550666999999997
Average (Standard dev.)0.01160014 (±1.1070261)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mycobacterium tuberculosis ATP synthase

EntireName: Mycobacterium tuberculosis ATP synthase
Components
  • Complex: Mycobacterium tuberculosis ATP synthase
    • 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 c
  • Protein or peptide: ATP synthase subunit a
  • Protein or peptide: ATP synthase subunit b
  • Protein or peptide: Multifunctional fusion protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: (1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol

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Supramolecule #1: Mycobacterium tuberculosis ATP synthase

SupramoleculeName: Mycobacterium tuberculosis ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mycobacterium tuberculosis (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: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 59.35807 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MAELTIPADD IQSAIEEYVS SFTADTSREE VGTVVDAGDG IAHVEGLPSV MTQELLEFPG GILGVALNLD EHSVGAVILG DFENIEEGQ QVKRTGEVLS VPVGDGFLGR VVNPLGQPID GRGDVDSDTR RALELQAPSV VHRQGVKEPL QTGIKAIDAM T PIGRGQRQ ...String:
MAELTIPADD IQSAIEEYVS SFTADTSREE VGTVVDAGDG IAHVEGLPSV MTQELLEFPG GILGVALNLD EHSVGAVILG DFENIEEGQ QVKRTGEVLS VPVGDGFLGR VVNPLGQPID GRGDVDSDTR RALELQAPSV VHRQGVKEPL QTGIKAIDAM T PIGRGQRQ LIIGDRKTGK TAVCVDTILN QRQNWESGDP KKQVRCVYVA IGQKGTTIAA VRRTLEEGGA MDYTTIVAAA AS ESAGFKW LAPYTGSAIA QHWMYEGKHV LIIFDDLTKQ AEAYRAISLL LRRPPGREAY PGDVFYLHSR LLERCAKLSD DLG GGSLTG LPIIETKAND ISAYIPTNVI SITDGQCFLE TDLFNQGVRP AINVGVSVSR VGGAAQIKAM KEVAGSLRLD LSQY RELEA FAAFASDLDA ASKAQLERGA RLVELLKQPQ SQPMPVEEQV VSIFLGTGGH LDSVPVEDVR RFETELLDHM RASEE EILT EIRDSQKLTE EAADKLTEVI KNFKKGFAAT GGGSVVPDEH VEALDEDKLA KEAVKVKKPA PKKKK

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: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 53.150934 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTTTAEKTDR PGKPGSSDTS GRVVRVTGPV VDVEFPRGSI PELFNALHAE ITFESLAKTL TLEVAQHLGD NLVRTISLQP TDGLVRGVE VIDTGRSISV PVGEGVKGHV FNALGDCLDE PGYGEKFEHW SIHRKPPAFE ELEPRTEMLE TGLKVVDLLT P YVRGGKIA ...String:
MTTTAEKTDR PGKPGSSDTS GRVVRVTGPV VDVEFPRGSI PELFNALHAE ITFESLAKTL TLEVAQHLGD NLVRTISLQP TDGLVRGVE VIDTGRSISV PVGEGVKGHV FNALGDCLDE PGYGEKFEHW SIHRKPPAFE ELEPRTEMLE TGLKVVDLLT P YVRGGKIA LFGGAGVGKT VLIQEMINRI ARNFGGTSVF AGVGERTREG NDLWVELAEA NVLKDTALVF GQMDEPPGTR MR VALSALT MAEWFRDEQG QDVLLFIDNI FRFTQAGSEV STLLGRMPSA VGYQPTLADE MGELQERITS TRGRSITSMQ AVY VPADDY TDPAPATTFA HLDATTELSR AVFSKGIFPA VDPLASSSTI LDPSVVGDEH YRVAQEVIRI LQRYKDLQDI IAIL GIDEL SEEDKQLVNR ARRIERFLSQ NMMAAEQFTG QPGSTVPVKE TIEAFDRLCK GDFDHVPEQA FFLIGGLDDL AKKAE SLGA KL

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: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 33.929332 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIARAQARL ESARPYAFEI TRMLTTLAAE AALDHPLLVE RPEPKRAGVL VVSSDRGLC GAYNANIFRR SEELFSLLRE AGKQPVLYVV GRKAQNYYSF RNWNITESWM GFSEQPTYEN AAEIASTLVD A FLLGTDNG ...String:
MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIARAQARL ESARPYAFEI TRMLTTLAAE AALDHPLLVE RPEPKRAGVL VVSSDRGLC GAYNANIFRR SEELFSLLRE AGKQPVLYVV GRKAQNYYSF RNWNITESWM GFSEQPTYEN AAEIASTLVD A FLLGTDNG EDQRSDSGEG VDELHIVYTE FKSMLSQSAE AHRIAPMVVE YVEEDIGPRT LYSFEPDATM LFESLLPRYL TT RVYAALL ESAASELASR QRAMKSATDN ADDLIKALTL MANRERQAQI TQEISEIVGG ANALAEAR

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: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.149744 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MAELNVEIVA VDRNIWSGTA KFLFTRTTVG EIGILPRHIP LVAQLVDDAM VRVEREGEKD LRIAVDGGFL SVTEEGVSIL AESAEFESE IDEAAAKQDS ESDDPRIAAR GRARLRAVGA ID

UniProtKB: ATP synthase epsilon chain

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Macromolecule #5: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 5 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.058423 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MDPTIAAGAL IGGGLIMAGG AIGAGIGDGV AGNALISGVA RQPEAQGRLF TPFFITVGLV EAAYFINLAF MALFVFATPV K

UniProtKB: ATP synthase subunit c

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Macromolecule #6: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 27.488436 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTETILAAQI EVGEHHTATW LGMTVNTDTV LSTAIAGLIV IALAFYLRAK VTSTDVPGGV QLFFEAITIQ MRNQVESAIG MRIAPFVLP LAVTIFVFIL ISNWLAVLPV QYTDKHGHTT ELLKSAAADI NYVLALALFV FVCYHTAGIW RRGIVGHPIK L LKGHVTLL ...String:
MTETILAAQI EVGEHHTATW LGMTVNTDTV LSTAIAGLIV IALAFYLRAK VTSTDVPGGV QLFFEAITIQ MRNQVESAIG MRIAPFVLP LAVTIFVFIL ISNWLAVLPV QYTDKHGHTT ELLKSAAADI NYVLALALFV FVCYHTAGIW RRGIVGHPIK L LKGHVTLL APINLVEEVA KPISLSLRLF GNIFAGGILV ALIALFPPYI MWAPNAIWKA FDLFVGAIQA FIFALLTILY FS QAMELEE EHH

UniProtKB: ATP synthase subunit a

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Macromolecule #7: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 18.345771 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MGEVSAIVLA ASQAAEEGGE SSNFLIPNGT FFVVLAIFLV VLAVIGTFVV PPILKVLRER DAMVAKTLAD NKKSDEQFAA AQADYDEAM TEARVQASSL RDNARADGRK VIEDARVRAE QQVASTLQTA HEQLKRERDA VELDLRAHVG TMSATLASRI L GVDLTASA ATR

UniProtKB: ATP synthase subunit b

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Macromolecule #8: Multifunctional fusion protein

MacromoleculeName: Multifunctional fusion protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 48.866648 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MSTFIGQLFG FAVIVYLVWR FIVPLVGRLM SARQDTVRQQ LADAAAAADR LAEASQAHTK ALEDAKSEAH RVVEEARTDA ERIAEQLEA QADVEAERIK MQGARQVDLI RAQLTRQLRL ELGHESVRQA RELVRNHVAD QAQQSATVDR FLDQLDAMAP A TADVDYPL ...String:
MSTFIGQLFG FAVIVYLVWR FIVPLVGRLM SARQDTVRQQ LADAAAAADR LAEASQAHTK ALEDAKSEAH RVVEEARTDA ERIAEQLEA QADVEAERIK MQGARQVDLI RAQLTRQLRL ELGHESVRQA RELVRNHVAD QAQQSATVDR FLDQLDAMAP A TADVDYPL LAKMRSASRR ALTSLVDWFG TMAQDLDHQG LTTLAGELVS VARLLDREAV VTRYLTVPAE DATPRIRLIE RL VSGKVGA PTLEVLRTAV SKRWSANSDL IDAIEHVSRQ ALLELAERAG QVDEVEDQLF RFSRILDVQP RLAILLGDCA VPA EGRVRL LRKVLERADS TVNPVVVALL SHTVELLRGQ AVEEAVLFLA EVAVARRGEI VAQVGAAAEL SDAQRTRLTE VLSR IYGHP VTVQLHIDAA LLGGLSIAVG DEVIDGTLSS RLAAAEARLP D

UniProtKB: Multifunctional fusion protein

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / 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 #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / 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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Macromolecule #12: (1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimet...

MacromoleculeName: (1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol
type: ligand / ID: 12 / Number of copies: 7 / Formula: UTI
Molecular weightTheoretical: 614.503 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81528
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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