9IO5 | pdb_00009io5

Cryo-EM structure of G1-ATPase dimer from Mycoplasma mobile gliding machinery


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Dimeric assembly of F 1 -like ATPase for the gliding motility of Mycoplasma.

Toyonaga, T.Kato, T.Kawamoto, A.Miyata, T.Kawakami, K.Fujita, J.Hamaguchi, T.Namba, K.Miyata, M.

(2025) Sci Adv 11: eadr9319-eadr9319

  • DOI: https://doi.org/10.1126/sciadv.adr9319
  • Primary Citation of Related Structures:  
    9IO5

  • PubMed Abstract: 

    Rotary ATPases, including F 1 F O -, V 1 V O -, and A 1 A O -ATPases, are molecular motors that exhibit rotational movements for energy conversion. In the gliding bacterium, Mycoplasma mobile , a dimeric F 1 -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 1 -like ATPase complex. The structure revealed an assembly distinct from those of dimeric F 1 F O -ATPases. The F 1 -like ATPase unit associated by two subunits GliD and GliE was named G 1 -ATPase as an R 1 domain of rotary ATPases. G 1 -β subunit, a homolog of the F 1 -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 1 -ATPase, suggesting a rotation based on the rotary catalytic mechanism. Overall, the cryo-EM structure provides insights into the mechanism through which G 1 -ATPase drives the Mycoplasma gliding motility.


  • Organizational Affiliation
    • Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G1-ATPase subunit beta
A, B, C, H, I
A, B, C, H, I, J
784Mycoplasma mobile 163KMutation(s): 0 
EC: 3.6.3.14
UniProt
Find proteins for Q6KIC3 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711))
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Go to UniProtKB:  Q6KIC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6KIC3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
G1-ATPase subunit alpha
D, E, F, K, L
D, E, F, K, L, M
528Mycoplasma mobile 163KMutation(s): 0 
EC: 3.6.3.14
UniProt
Find proteins for Q6KIC4 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711))
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6KIC4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
G1-ATPase subunit gamma
G, N
336Mycoplasma mobile 163KMutation(s): 0 
UniProt
Find proteins for Q6KIC7 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711))
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UniProt GroupQ6KIC7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate kinase
O, P, Q
511Mycoplasma mobile 163KMutation(s): 0 
EC: 2.7.2.3
UniProt
Find proteins for Q6KHJ1 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711))
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UniProt GroupQ6KHJ1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
G1-ATPase subunit D
R, S, T, U, V
R, S, T, U, V, W
293Mycoplasma mobile 163KMutation(s): 0 
UniProt
Find proteins for Q6KIC8 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711))
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UniProt GroupQ6KIC8
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
G1-ATPase subunit E112Mycoplasma mobile 163KMutation(s): 0 
UniProt
Find proteins for Q6KHS6 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711))
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UniProt GroupQ6KHS6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UNKNOWN HELIX13Mycoplasma mobile 163KMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
UNKNOWN HELIX9Mycoplasma mobile 163KMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth A]
FA [auth D]
HA [auth E]
JA [auth F]
LA [auth H]
AA [auth A],
FA [auth D],
HA [auth E],
JA [auth F],
LA [auth H],
QA [auth K],
SA [auth L],
UA [auth M]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
DA [auth B],
OA [auth I]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
EA [auth B],
PA [auth I]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth A]
CA [auth B]
GA [auth D]
IA [auth E]
KA [auth F]
BA [auth A],
CA [auth B],
GA [auth D],
IA [auth E],
KA [auth F],
MA [auth H],
NA [auth I],
RA [auth K],
TA [auth L],
VA [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC3.3.2
RECONSTRUCTIONRELION4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP17H01544
Japan Science and TechnologyJapanJPMJCR19S5
Japan Agency for Medical Research and Development (AMED)JapanJP22am121003
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release