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- PDB-7njv: Mycobacterium smegmatis ATP synthase Fo combined class 2 -

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Basic information

Entry
Database: PDB / ID: 7njv
TitleMycobacterium smegmatis ATP synthase Fo combined class 2
Components
  • ATP synthase subunit a
  • ATP synthase subunit b-delta
  • ATP synthase subunit b
  • ATP synthase subunit c
KeywordsHYDROLASE / complex / synthase
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / hydrolase activity / integral component of membrane / plasma membrane
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 b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase a subunit signature. / ATP synthase A chain / ATP synthase, F0 complex, subunit A superfamily / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A ...ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase a subunit signature. / ATP synthase A chain / ATP synthase, F0 complex, subunit A superfamily / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase c subunit signature. / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase subunit C / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily
Similarity search - Domain/homology
ATP synthase subunit c / Bedaquiline / ATP synthase subunit b / ATP synthase subunit b-delta / ATP synthase subunit a
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMontgomery, M.G. / Petri, J. / Spikes, T.E. / Walker, J.E.
Funding support United Kingdom, 2items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
L: ATP synthase subunit c
M: ATP synthase subunit c
N: ATP synthase subunit c
O: ATP synthase subunit c
P: ATP synthase subunit c
Q: ATP synthase subunit c
R: ATP synthase subunit c
S: ATP synthase subunit c
T: ATP synthase subunit c
a: ATP synthase subunit a
b: ATP synthase subunit b
d: ATP synthase subunit b-delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,02913
Polymers171,47312
Non-polymers5561
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ATP synthase subunit c / / ATP synthase F(0) sector subunit c / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 8597.982 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: atpE, MSMEG_4941 / Production host: Mycolicibacterium smegmatis (bacteria) / Strain (production host): mc2 4517 / References: UniProt: A0R205
#2: Protein ATP synthase subunit a / / ATP synthase F0 sector subunit a / F-ATPase subunit 6


Mass: 27568.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: atpB, MSMEG_4942 / Production host: Mycolicibacterium smegmatis (bacteria) / Strain (production host): mc2 4517 / References: UniProt: A0R206
#3: Protein ATP synthase subunit b / / ATP synthase F(0) sector subunit b / ATPase subunit I / F-type ATPase subunit b / F-ATPase subunit b


Mass: 19018.170 Da / Num. of mol.: 1 / Mutation: C-ter 10His tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: atpF, MSMEG_4940, MSMEI_4813 / Production host: Mycolicibacterium smegmatis (bacteria) / Strain (production host): mc2 4517 / References: UniProt: A0R204
#4: Protein ATP synthase subunit b-delta /


Mass: 47504.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: atpFH, atpF, atpH, MSMEG_4939, MSMEI_4812 / Production host: Mycolicibacterium smegmatis (bacteria) / Strain (production host): mc2 4517 / References: UniProt: A0R203
#5: Chemical ChemComp-BQ1 / Bedaquiline / Bedaquiline


Mass: 555.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H31BrN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mycobacterium smegmatis ATP synthase / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.547 MDa / Experimental value: YES
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: mc2 4517
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 59.86 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46961 / Symmetry type: POINT

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