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- EMDB-12439: Mycobacterium smegmatis ATP synthase F1 state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-12439
TitleMycobacterium smegmatis ATP synthase F1 state 2
Map dataMsmeg ATP synthase F1 state 2 map
Sample
  • Complex: Mycobacterium smegmatis ATP synthase
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water
Keywordscomplex / synthase / HYDROLASE
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit ...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, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / 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 beta / ATP synthase gamma chain / ATP synthase subunit alpha
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsMontgomery MG / Petri J / Spikes TE / Walker JE
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00015/8 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structure of the ATP synthase from provides targets for treating tuberculosis.
Authors: Martin G Montgomery / Jessica Petri / Tobias E Spikes / John E Walker /
Abstract: The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from This analysis confirms features in a prior description of the structure of the enzyme, ...The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a "fail-safe" mechanism involving the b'-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated "fail-safe" mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel.
History
DepositionFeb 18, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nkh
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12439.png

Downloads & links

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Map

FileDownload / File: emd_12439.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMsmeg ATP synthase F1 state 2 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 415. Å		0.83 Å/pix.
x 500 pix.
= 415. Å		0.83 Å/pix.
x 500 pix.
= 415. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0167 / Movie #1: 0.0167
Minimum - Maximum-0.022639628 - 0.07924864
Average (Standard dev.)0.00006846325 (±0.0012074445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 415.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z415.000415.000415.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0230.0790.000

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Supplemental data

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Sample components

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Entire : Mycobacterium smegmatis ATP synthase

EntireName: Mycobacterium smegmatis ATP synthase
Components
  • Complex: Mycobacterium smegmatis ATP synthase
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Mycobacterium smegmatis ATP synthase

SupramoleculeName: Mycobacterium smegmatis ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 547 KDa

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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: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 58.951461 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MAELTISAAD IEGAIEDYVS SFSADTEREE IGTVIDAGDG IAHVEGLPSV MTQELLEFPG GVLGVALNLD EHSVGAVILG EFEKIEEGQ QVKRTGEVLS VPVGDAFLGR VVNPLGQPID GQGDIAAETR RALELQAPSV VQRQSVSEPL QTGIKAIDAM T PIGRGQRQ ...String:
MAELTISAAD IEGAIEDYVS SFSADTEREE IGTVIDAGDG IAHVEGLPSV MTQELLEFPG GVLGVALNLD EHSVGAVILG EFEKIEEGQ QVKRTGEVLS VPVGDAFLGR VVNPLGQPID GQGDIAAETR RALELQAPSV VQRQSVSEPL QTGIKAIDAM T PIGRGQRQ LIIGDRKTGK TAVCVDTILN QREAWLTGDP KQQVRCVYVA IGQKGTTIAS VKRALEEGGA MEYTTIVAAP AS DAAGFKW LAPYTGSAIG QHWMYNGKHV LIVFDDLSKQ ADAYRAISLL LRRPPGREAF PGDVFYLHSR LLERCAKLSD ELG GGSMTG LPIIETKAND ISAFIPTNVI SITDGQCFLE SDLFNQGVRP AINVGVSVSR VGGAAQIKAM KEVAGSLRLD LSQY RELEA FAAFASDLDA ASKAQLDRGA RLVELLKQPQ YSPLAVEEQV VAIFLGTQGH LDSVPVEDVQ RFESELLEHV KASHS DIFD GIRETKKLSE EAEEKLVSVI NEFKKGFQAS DGSSVVVSEN AEALDPEDLE KESVKVRKPA PKKA

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: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 51.670453 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTATAEKTAG RVVRITGPVV DVEFPRGSVP ELFNALHAEI TFGALAKTLT LEVAQHLGDS LVRCISMQPT DGLVRGVEVT DTGASISVP VGDGVKGHVF NALGDCLDDP GYGKDFEHWS IHRKPPAFSD LEPRTEMLET GLKVVDLLTP YVRGGKIALF G GAGVGKTV ...String:
MTATAEKTAG RVVRITGPVV DVEFPRGSVP ELFNALHAEI TFGALAKTLT LEVAQHLGDS LVRCISMQPT DGLVRGVEVT DTGASISVP VGDGVKGHVF NALGDCLDDP GYGKDFEHWS IHRKPPAFSD LEPRTEMLET GLKVVDLLTP YVRGGKIALF G GAGVGKTV LIQEMINRIA RNFGGTSVFA GVGERTREGN DLWVELADAN VLKDTALVFG QMDEPPGTRM RVALSALTMA EF FRDEQGQ DVLLFIDNIF RFTQAGSEVS TLLGRMPSAV GYQPTLADEM GELQERITST RGRSITSMQA VYVPADDYTD PAP ATTFAH LDATTELSRA VFSKGIFPAV DPLASSSTIL DPAIVGDEHY RVAQEVIRIL QRYKDLQDII AILGIDELSE EDKQ LVNRA RRIERFLSQN MMAAEQFTGQ PGSTVPLKET IEAFDKLTKG EFDHLPEQAF FLIGGLDDLA KKAESLGAKL

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 / Details: Alignment is incorrect. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 33.439836 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIAKAQARV EAARPYAAEI TNMLTELAGA SALDHPLLVE RKQPKRAGVL VVSSDRGLC GAYNANVLRR AEELFSLLRD EGKDPVLYVV GRKALGYFSF RQRTVVESWT GFSERPTYEN AREIADTLVN A FMAGADDE ...String:
MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIAKAQARV EAARPYAAEI TNMLTELAGA SALDHPLLVE RKQPKRAGVL VVSSDRGLC GAYNANVLRR AEELFSLLRD EGKDPVLYVV GRKALGYFSF RQRTVVESWT GFSERPTYEN AREIADTLVN A FMAGADDE GDDAGADGIL GVDELHIVFT EFRSMLSQTA VARRAAPMEV EYVGEVETGP RTLYSFEPDP ETLFDALLPR YI ATRVYAA LLEAAASESA SRRRAMKSAT DNADDLIKAL TLAANRERQA QITQEISEIV GGANALAGSK

UniProtKB: ATP synthase gamma chain

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / 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 #5: MAGNESIUM ION

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

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / 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 #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 16 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.86 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24938
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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