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- PDB-7vaq: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state3-2 -

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Basic information

Entry
Database: PDB / ID: 7vaq
TitleV1EG of V/A-ATPase from Thermus thermophilus, high ATP, state3-2
Components(V-type ATP synthase ...) x 6
KeywordsMOTOR PROTEIN / rotary ATPase / V-type ATPase / ATP synthase / Thermus thermophilus / chemo-mechanical coupling
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / metal ion binding
Similarity search - Function
Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit ...Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / V-type ATP synthase subunit D / V-type ATP synthase subunit E / V-type ATP synthase subunit F / V-type ATP synthase alpha chain / V-type ATP synthase beta chain / V-type ATP synthase, subunit (VAPC-THERM)
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKishikawa, J. / Nakanishi, A. / Nakano, A. / Saeki, S. / Furuta, A. / Kato, T. / Mitsuoka, K. / Yokoyama, K.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03231 Japan
Japan Society for the Promotion of Science (JSPS)20K06514 Japan
Japan Society for the Promotion of Science (JSPS)20J00162 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)12024046 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)20215008 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases.
Authors: J Kishikawa / A Nakanishi / A Nakano / S Saeki / A Furuta / T Kato / K Mistuoka / K Yokoyama /
Abstract: V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FF ATP synthase. When powered by ATP hydrolysis, the V domain rotates the central rotor against the AB hexamer, ...V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FF ATP synthase. When powered by ATP hydrolysis, the V domain rotates the central rotor against the AB hexamer, composed of three catalytic AB dimers adopting different conformations (AB, AB, and AB). Here, we report the atomic models of 18 catalytic intermediates of the V domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not rotate immediately after binding of ATP to the V. Instead, three events proceed simultaneously with the 120˚ rotation of the shaft: hydrolysis of ATP in AB, zipper movement in AB by the binding ATP, and unzipper movement in AB with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in AB, rather than the power stroke model proposed previously for F-ATPase.
History
DepositionAug 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type ATP synthase alpha chain
B: V-type ATP synthase alpha chain
C: V-type ATP synthase alpha chain
D: V-type ATP synthase beta chain
E: V-type ATP synthase beta chain
F: V-type ATP synthase beta chain
G: V-type ATP synthase subunit D
H: V-type ATP synthase subunit F
I: V-type ATP synthase subunit G
J: V-type ATP synthase subunit E
K: V-type ATP synthase subunit G
L: V-type ATP synthase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,88818
Polymers454,30212
Non-polymers1,5856
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area47710 Å2
ΔGint-266 kcal/mol
Surface area141690 Å2

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Components

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V-type ATP synthase ... , 6 types, 12 molecules ABCDEFGHIKJL

#1: Protein V-type ATP synthase alpha chain / V-ATPase subunit A


Mass: 63669.957 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8
References: UniProt: Q56403, H+-transporting two-sector ATPase
#2: Protein V-type ATP synthase beta chain / V-ATPase subunit B


Mass: 53219.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q56404
#3: Protein V-type ATP synthase subunit D / V-ATPase subunit D


Mass: 24715.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: O87880
#4: Protein V-type ATP synthase subunit F / V-ATPase subunit F


Mass: 11294.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: P74903
#5: Protein V-type ATP synthase subunit G


Mass: 13166.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q5SIT5
#6: Protein V-type ATP synthase subunit E / V-ATPase subunit E


Mass: 20645.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: P74901

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Non-polymers , 4 types, 6 molecules

#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Sequence detailsFor V-ATPase subunit A, the bacterium has two mutations in its genome (S232A and T235S).

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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: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state3-2
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Buffer solutionpH: 8
Buffer componentConc.: 6 mM / Name: ATP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 0.042 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2300834
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5300 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: The atomic model built in this study was used as an initial model.
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00330114
ELECTRON MICROSCOPYf_angle_d0.4840814
ELECTRON MICROSCOPYf_dihedral_angle_d4.1084189
ELECTRON MICROSCOPYf_chiral_restr0.0424572
ELECTRON MICROSCOPYf_plane_restr0.0045333

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