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- PDB-6n2d: Bacillus PS3 ATP synthase membrane region -

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Basic information

Entry
Database: PDB / ID: 6n2d
TitleBacillus PS3 ATP synthase membrane region
Components
  • ATP synthase subunit a
  • ATP synthase subunit b
  • ATP synthase subunit c
KeywordsHYDROLASE
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase subunit c
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGuo, H. / Rubinstein, J.L.
Funding support Canada, Japan, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 81294 Canada
Japan Society for the Promotion of Science (JSPS)JP18H02409 Japan
CitationJournal: Elife / Year: 2019
Title: Structure of a bacterial ATP synthase.
Authors: Hui Guo / Toshiharu Suzuki / John L Rubinstein /
Abstract: ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest ...ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed the PS3 ATP synthase in , purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunit shows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme.
History
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / cell / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
b2: ATP synthase subunit b
b1: ATP synthase subunit b
a: ATP synthase subunit a
c0: ATP synthase subunit c
c1: ATP synthase subunit c
c2: ATP synthase subunit c
c3: ATP synthase subunit c
c4: ATP synthase subunit c
c5: ATP synthase subunit c
c6: ATP synthase subunit c
c7: ATP synthase subunit c
c8: ATP synthase subunit c
c9: ATP synthase subunit c


Theoretical massNumber of molelcules
Total (without water)138,32513
Polymers138,32513
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area37560 Å2
ΔGint-426 kcal/mol
Surface area35320 Å2

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Components

#1: 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: 19249.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Strain: PS3 / Gene: atpF / Production host: Escherichia coli (E. coli)
#2: Protein ATP synthase subunit a / / ATP synthase F0 sector subunit a / F-ATPase subunit 6


Mass: 26449.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Strain: PS3 / Gene: atpB / Production host: Escherichia coli (E. coli)
#3: 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: 7337.780 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Strain: PS3 / Gene: atpE, uncE / Production host: Escherichia coli (E. coli) / References: UniProt: P00845

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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: Membrane-embedded region of Bacillus PS3 ATP synthase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 110 kDa/nm / Experimental value: NO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 4 K

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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 / Nominal magnification: 75000 X / Calibrated magnification: 132075 X / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 0.71 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: (1.13_2998: phenix.real_space_refine) / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
9cryoSPARC2initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1238140
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 895574 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 91.12 / Protocol: AB INITIO MODEL / Space: REAL

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