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- EMDB-12438: Mycobacterium smegmatis ATP synthase b-delta state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-12438
TitleMycobacterium smegmatis ATP synthase b-delta state 1
Map data
SampleMycobacterium smegmatis ATP synthase:
(ATP synthase subunit ...) x 4
Function / homology
Function and homology information


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 / integral component of membrane / 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 B/B' CF(0) / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase delta (OSCP) subunit / ATPase, OSCP/delta subunit / ATP synthase, F1 complex, beta subunit / ATP synthase alpha/beta chain, C terminal domain / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal ...ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase delta (OSCP) subunit / ATPase, OSCP/delta subunit / ATP synthase, F1 complex, beta subunit / ATP synthase alpha/beta chain, C terminal domain / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, alpha subunit / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATP synthase alpha and beta subunits signature. / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / 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 subunit alpha / ATP synthase subunit b-delta / ATP synthase subunit b
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria) / Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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 17, 2021-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0177
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0177
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nkd
  • Surface level: 0.0177
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12438.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 0.0177 / Movie #1: 0.0177
Minimum - Maximum-0.022559846 - 0.0675866
Average (Standard dev.)1.6086007e-05 (±0.00045761908)
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-0.0230.0680.000

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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 / Number of Components: 5

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Component #1: protein, Mycobacterium smegmatis ATP synthase

ProteinName: Mycobacterium smegmatis ATP synthase / Recombinant expression: No
MassExperimental: 547 kDa
SourceSpecies: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (engineered)Expression System: Mycolicibacterium smegmatis (bacteria) / Strain: mc2 4517

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Component #2: protein, ATP synthase subunit alpha

ProteinName: ATP synthase subunit alpha / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 58.951461 kDa
SourceSpecies: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Source (engineered)Expression System: Mycolicibacterium smegmatis (bacteria)

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Component #3: protein, ATP synthase subunit beta

ProteinName: ATP synthase subunit beta
Details: Poor alignment on Chain F there is no sequence conflict. DSLV is from res59, RGV is from res75
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 51.670453 kDa
SourceSpecies: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Source (engineered)Expression System: Mycolicibacterium smegmatis (bacteria)

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Component #4: protein, ATP synthase subunit b-delta

ProteinName: ATP synthase subunit b-delta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.504723 kDa
SourceSpecies: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Source (engineered)Expression System: Mycolicibacterium smegmatis (bacteria)

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Component #5: protein, ATP synthase subunit b

ProteinName: ATP synthase subunit b / Details: C-ter 10His tag / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.01817 kDa
SourceSpecies: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Source (engineered)Expression System: Mycolicibacterium smegmatis (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 59.86 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 127186
3D reconstructionResolution: 3.12 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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