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- EMDB-12444: Mycobacterium smegmatis ATP synthase rotor state 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-12444
TitleMycobacterium smegmatis ATP synthase rotor state 3
Map dataMsmeg ATP synthase rotor state 3 map
Sample
  • Complex: Mycobacterium smegmatis ATP synthase
    • 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 alpha
Keywordscomplex / synthase / HYDROLASE
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / 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 / hydrolase activity / lipid binding / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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, F0 complex, subunit C, bacterial/chloroplast / 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, 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase epsilon chain / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit c
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) / Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsMontgomery MG / Petri J
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: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nkn
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12444.png

Downloads & links

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Map

FileDownload / File: emd_12444.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMsmeg ATP synthase rotor state 3 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: 0.021 / Movie #1: 0.021
Minimum - Maximum-0.03219788 - 0.073817104
Average (Standard dev.)0.00003573808 (±0.00082661567)
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-0.0320.0740.000

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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 gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit alpha

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Supramolecule #1: Mycobacterium smegmatis ATP synthase

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

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Macromolecule #1: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
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 #2: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.277741 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MADLNVEIVA VERELWSGPA TFVFTRTTAG EIGILPRHIP LVAQLVDDAM VRVEREGEDD LRIAVDGGFL SVTEETVRIL VENAQFESE IDADAAKEDA ASDDERTAAW GRARLRALGQ ID

UniProtKB: ATP synthase epsilon chain

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Macromolecule #3: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 3 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 8.597982 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MDLDPNAIIT AGALIGGGLI MGGGAIGAGI GDGIAGNALI SGIARQPEAQ GRLFTPFFIT VGLVEAAYFI NLAFMALFVF ATPGLQ

UniProtKB: ATP synthase subunit c

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Macromolecule #4: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
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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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: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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