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- PDB-9io5: Cryo-EM structure of G1-ATPase dimer from Mycoplasma mobile glidi... -

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Basic information

Entry
Database: PDB / ID: 9io5
TitleCryo-EM structure of G1-ATPase dimer from Mycoplasma mobile gliding machinery
Components
  • (G1-ATPase subunit ...) x 5
  • (UNKNOWN HELIX) x 2
  • Phosphoglycerate kinase
KeywordsHYDROLASE / ATPase / Complex / kinase / Ring
Function / homology
Function and homology information


H+-transporting two-sector ATPase / phosphoglycerate kinase / phosphoglycerate kinase activity / : / proton-transporting ATP synthase activity, rotational mechanism / gluconeogenesis / glycolytic process / ADP binding / hydrolase activity / ATP hydrolysis activity ...H+-transporting two-sector ATPase / phosphoglycerate kinase / phosphoglycerate kinase activity / : / proton-transporting ATP synthase activity, rotational mechanism / gluconeogenesis / glycolytic process / ADP binding / hydrolase activity / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / ATP synthase, F1 complex, beta subunit / : / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit ...Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / ATP synthase, F1 complex, beta subunit / : / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Phosphoglycerate kinase / Uncharacterized protein / ATP synthase beta chain / ATP synthase alpha chain / Expressed protein / Expressed protein
Similarity search - Component
Biological speciesMycoplasma mobile 163K (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsToyonaga, T. / Kato, T. / Kawamoto, A. / Miyata, T. / Kawakami, K. / Fujita, J. / Hamaguchi, T. / Namba, K. / Miyata, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H01544 Japan
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Agency for Medical Research and Development (AMED)JP22am121003 Japan
Other government
CitationJournal: Sci Adv / Year: 2025
Title: Dimeric assembly of F-like ATPase for the gliding motility of .
Authors: Takuma Toyonaga / Takayuki Kato / Akihiro Kawamoto / Tomoko Miyata / Keisuke Kawakami / Junso Fujita / Tasuku Hamaguchi / Keiichi Namba / Makoto Miyata /
Abstract: Rotary ATPases, including FF-, VV-, and AA-ATPases, are molecular motors that exhibit rotational movements for energy conversion. In the gliding bacterium, , a dimeric F-like ATPase forms a chain ...Rotary ATPases, including FF-, VV-, and AA-ATPases, are molecular motors that exhibit rotational movements for energy conversion. In the gliding bacterium, , a dimeric F-like ATPase forms a chain structure within the cell, which is proposed to drive the gliding motility. However, the mechanisms of force generation and transmission remain unclear. We determined the electron cryomicroscopy (cryo-EM) structure of the dimeric F-like ATPase complex. The structure revealed an assembly distinct from those of dimeric FF-ATPases. The F-like ATPase unit associated by two subunits GliD and GliE was named G-ATPase as an R domain of rotary ATPases. G-β subunit, a homolog of the F-ATPase catalytic subunit, exhibited a specific N-terminal region that incorporates the glycolytic enzyme, phosphoglycerate kinase into the complex. Structural features of the ATPase displayed strong similarities to F-ATPase, suggesting a rotation based on the rotary catalytic mechanism. Overall, the cryo-EM structure provides insights into the mechanism through which G-ATPase drives the gliding motility.
History
DepositionJul 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G1-ATPase subunit beta
B: G1-ATPase subunit beta
C: G1-ATPase subunit beta
D: G1-ATPase subunit alpha
E: G1-ATPase subunit alpha
F: G1-ATPase subunit alpha
G: G1-ATPase subunit gamma
H: G1-ATPase subunit beta
I: G1-ATPase subunit beta
J: G1-ATPase subunit beta
K: G1-ATPase subunit alpha
L: G1-ATPase subunit alpha
M: G1-ATPase subunit alpha
N: G1-ATPase subunit gamma
O: Phosphoglycerate kinase
P: Phosphoglycerate kinase
Q: Phosphoglycerate kinase
R: G1-ATPase subunit D
S: G1-ATPase subunit D
T: G1-ATPase subunit D
U: G1-ATPase subunit D
V: G1-ATPase subunit D
W: G1-ATPase subunit D
X: G1-ATPase subunit E
Y: UNKNOWN HELIX
Z: UNKNOWN HELIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,356,53548
Polymers1,351,19026
Non-polymers5,34522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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G1-ATPase subunit ... , 5 types, 21 molecules ABCHIJDEFKLMGNRSTUVWX

#1: Protein
G1-ATPase subunit beta


Mass: 88510.383 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
References: UniProt: Q6KIC3, H+-transporting two-sector ATPase
#2: Protein
G1-ATPase subunit alpha


Mass: 58794.668 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
References: UniProt: Q6KIC4, H+-transporting two-sector ATPase
#3: Protein G1-ATPase subunit gamma


Mass: 39810.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521 / References: UniProt: Q6KIC7
#5: Protein
G1-ATPase subunit D


Mass: 33753.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521 / References: UniProt: Q6KIC8
#6: Protein G1-ATPase subunit E


Mass: 13264.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521 / References: UniProt: Q6KHS6

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Protein , 1 types, 3 molecules OPQ

#4: Protein Phosphoglycerate kinase


Mass: 56680.750 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521 / References: UniProt: Q6KHJ1, phosphoglycerate kinase

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Protein/peptide , 2 types, 2 molecules YZ

#7: Protein/peptide UNKNOWN HELIX


Mass: 1124.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
#8: Protein/peptide UNKNOWN HELIX


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521

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Non-polymers , 4 types, 22 molecules

#9: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#12: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: G1-ATPase dimer from Mycoplasma mobile gliding machinery
Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Mycoplasma mobile 163K (bacteria) / Strain: P476R gli521
Buffer solutionpH: 7.3
Buffer component
IDConc.NameFormulaBuffer-ID
18.1 mMdisodium hydrogenphosphateNa2HPO41
21.5 mMpotassium dihydrogen phosphateKH2PO41
32.7 mMpotassium chlorideKCl1
4137 mMsodium chlorideNaCl1
51 mMmagnesium chlorideMgCl21
60.1 %CHAPSC32H58N2O7S1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Epoxidized graphene grid (EG-grid) was used. / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 3.3 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7350
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC3.3.2particle selection
2SerialEMimage acquisition
4cryoSPARC3.3.2CTF correction
7UCSF Chimera1.15model fitting
9PHENIX1.19model refinement
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
14RELION43D reconstructionMask creation and post-processing were done in RELION 4.0.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 633820
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142490 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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