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Structure paper

TitleStructure of the ATP synthase from provides targets for treating tuberculosis.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 118, Issue 47, Year 2021
Publish dateNov 23, 2021
AuthorsMartin G Montgomery / Jessica Petri / Tobias E Spikes / John E Walker /
PubMed AbstractThe 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.
External linksProc Natl Acad Sci U S A / PubMed:34782468
MethodsEM (single particle)
Resolution2.11 - 4.32 Å
Structure data

EMDB-12377, PDB-7njk:
Mycobacterium smegmatis ATP synthase state 1a
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-12378:
Mycobacterium smegmatis ATP synthase F1 state 1a
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-12379:
Mycobacterium smegmatis ATP synthase Fo state 1a
Method: EM (single particle) / Resolution: 3.37 Å

EMDB-12380:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 1a
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-12381:
Mycobacterium smegmatis ATP synthase b-delta state 1a
Method: EM (single particle) / Resolution: 3.24 Å

EMDB-12382, PDB-7njl:
Mycobacterium smegmatis ATP synthase state 1b
Method: EM (single particle) / Resolution: 2.71 Å

EMDB-12383:
Mycobacterium smegmatis ATP synthase F1 state 1b
Method: EM (single particle) / Resolution: 2.71 Å

EMDB-12384:
Mycobacterium smegmatis ATP synthase Fo state 1b
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-12385:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 1b
Method: EM (single particle) / Resolution: 3.77 Å

EMDB-12386:
Mycobacterium smegmatis ATP synthase b-delta state 1b
Method: EM (single particle) / Resolution: 3.84 Å

EMDB-12387, PDB-7njm:
Mycobacterium smegmatis ATP synthase state 1c
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-12388:
Mycobacterium smegmatis ATP synthase F1 state 1c
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-12389:
Mycobacterium smegmatis ATP synthase Fo state 1c
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-12390:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 1c
Method: EM (single particle) / Resolution: 3.87 Å

EMDB-12391:
Mycobacterium smegmatis ATP synthase b-delta state 1c
Method: EM (single particle) / Resolution: 3.73 Å

EMDB-12392, PDB-7njn:
Mycobacterium smegmatis ATP synthase state 1d
Method: EM (single particle) / Resolution: 2.64 Å

EMDB-12393:
Mycobacterium smegmatis ATP synthase F1 state 1d
Method: EM (single particle) / Resolution: 2.64 Å

EMDB-12394:
Mycobacterium smegmatis ATP synthase Fo state 1d
Method: EM (single particle) / Resolution: 3.74 Å

EMDB-12395:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 1d
Method: EM (single particle) / Resolution: 3.99 Å

EMDB-12396:
Mycobacterium smegmatis ATP synthase b-delta state 1d
Method: EM (single particle) / Resolution: 3.61 Å

EMDB-12397, PDB-7njo:
Mycobacterium smegmatis ATP synthase state 1e
Method: EM (single particle) / Resolution: 2.92 Å

EMDB-12398:
Mycobacterium smegmatis ATP synthase F1 state 1e
Method: EM (single particle) / Resolution: 2.92 Å

EMDB-12399:
Mycobacterium smegmatis ATP synthase Fo state 1e
Method: EM (single particle) / Resolution: 3.92 Å

EMDB-12400:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 1e
Method: EM (single particle) / Resolution: 4.15 Å

EMDB-12401:
Mycobacterium smegmatis ATP synthase b-delta state 1e
Method: EM (single particle) / Resolution: 3.99 Å

EMDB-12402, PDB-7njp:
Mycobacterium smegmatis ATP synthase state 2
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-12403:
Mycobacterium smegmatis ATP synthase F1 state 2
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-12404, PDB-7nkp:
Mycobacterium smegmatis ATP synthase Fo state 2
Method: EM (single particle) / Resolution: 4.06 Å

EMDB-12405:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 2
Method: EM (single particle) / Resolution: 4.06 Å

EMDB-12406, PDB-7nkl:
Mycobacterium smegmatis ATP synthase b-delta state 2
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-12407, PDB-7njq:
Mycobacterium smegmatis ATP synthase state 3a
Method: EM (single particle) / Resolution: 2.67 Å

EMDB-12408:
Mycobacterium smegmatis ATP synthase F1 state 3a
Method: EM (single particle) / Resolution: 2.67 Å

EMDB-12409:
Mycobacterium smegmatis ATP synthase Fo state 3a
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-12410:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 3a
Method: EM (single particle) / Resolution: 3.43 Å

EMDB-12411:
Mycobacterium smegmatis ATP synthase b-delta state 3a
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-12412, PDB-7njr:
Mycobacterium smegmatis ATP synthase state 3b
Method: EM (single particle) / Resolution: 2.56 Å

EMDB-12413:
Mycobacterium smegmatis ATP synthase F1 state 3b
Method: EM (single particle) / Resolution: 2.56 Å

EMDB-12414:
Mycobacterium smegmatis ATP synthase Fo state 3b
Method: EM (single particle) / Resolution: 3.29 Å

EMDB-12415:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 3b
Method: EM (single particle) / Resolution: 3.42 Å

EMDB-12416:
Mycobacterium smegmatis ATP synthase b-delta state 3b
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-12417, PDB-7njs:
Mycobacterium smegmatis ATP synthase state 3c
Method: EM (single particle) / Resolution: 2.46 Å

EMDB-12418:
Mycobacterium smegmatis ATP synthase F1 state 3c
Method: EM (single particle) / Resolution: 2.46 Å

EMDB-12419:
Mycobacterium smegmatis ATP synthase Fo state 3c
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-12420:
Mycobacterium smegmatis ATP synthase Peripheral Stalk state 3c
Method: EM (single particle) / Resolution: 3.29 Å

EMDB-12421:
Mycobacterium smegmatis ATP synthase b-delta state 3c
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-12422, PDB-7njt:
Mycobacterium smegmatis ATP synthase Fo combined all classes
Method: EM (single particle) / Resolution: 2.75 Å

EMDB-12423, PDB-7nju:
Mycobacterium smegmatis ATP synthase Fo combined class 1
Method: EM (single particle) / Resolution: 3.74 Å

EMDB-12424, PDB-7njv:
Mycobacterium smegmatis ATP synthase Fo combined class 2
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-12425, PDB-7njw:
Mycobacterium smegmatis ATP synthase Fo combined class 3
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-12426, PDB-7njx:
Mycobacterium smegmatis ATP synthase Fo combined class 4
Method: EM (single particle) / Resolution: 4.32 Å

EMDB-12427, PDB-7njy:
Mycobacterium smegmatis ATP synthase Fo combined class 5
Method: EM (single particle) / Resolution: 2.94 Å

EMDB-12432, PDB-7nk7:
Mycobacterium smegmatis ATP synthase F1 state 1
Method: EM (single particle) / Resolution: 2.11 Å

EMDB-12434, PDB-7nk9:
Mycobacterium smegmatis ATP synthase Fo domain state 1
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-12436, PDB-7nkb:
Mycobacterium smegmatis ATP synthase rotor state 1
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-12438, PDB-7nkd:
Mycobacterium smegmatis ATP synthase b-delta state 1
Method: EM (single particle) / Resolution: 3.12 Å

EMDB-12439, PDB-7nkh:
Mycobacterium smegmatis ATP synthase F1 state 2
Method: EM (single particle) / Resolution: 2.78 Å

EMDB-12441, PDB-7nkj:
Mycobacterium smegmatis ATP synthase F1 state 3
Method: EM (single particle) / Resolution: 2.17 Å

EMDB-12442, PDB-7nkk:
Mycobacterium smegmatis ATP synthase rotor state 2
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-12444, PDB-7nkn:
Mycobacterium smegmatis ATP synthase rotor state 3
Method: EM (single particle) / Resolution: 2.71 Å

EMDB-12446, PDB-7nkq:
Mycobacterium smegmatis ATP synthase b-delta state 3
Method: EM (single particle) / Resolution: 2.98 Å

EMDB-12461, PDB-7nl9:
Mycobacterium smegmatis ATP synthase Fo state 3
Method: EM (single particle) / Resolution: 2.86 Å

Chemicals

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

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-HOH:
WATER / Water

ChemComp-BQ1:
Bedaquiline / medication, antibiotic*YM / Bedaquiline

Source
  • mycolicibacterium smegmatis mc2 155 (bacteria)
  • mycolicibacterium smegmatis (strain atcc 700084 / mc(2)155) (bacteria)
  • mycobacterium smegmatis (strain atcc 700084 / mc(2)155) (bacteria)
  • Mycolicibacterium smegmatis (bacteria)
KeywordsHYDROLASE / complex / synthase

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