9IO5 | pdb_00009io5

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

PDB DOI: https://doi.org/10.2210/pdb9IO5/pdb
EM Map EMD-60718: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Mycoplasma mobile 163K
Mutation(s): No

Deposited: 2024-07-08 Released: 2025-03-12
Deposition Author(s): Toyonaga, T., Kato, T., Kawamoto, A., Miyata, T., Kawakami, K., Fujita, J., Hamaguchi, T., Namba, K., Miyata, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Japan Agency for Medical Research and Development (AMED), Other government

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

PubMed: 40009674 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adr9319
Primary Citation Related Structures:
9IO5

PubMed Abstract:
Rotary ATPases, including F ₁F _O-, V ₁V _O-, and A ₁A _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 ₁F _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.

Macromolecule Content

Total Structure Weight: 1,356.53 kDa
Atom Count: 69,678
Modeled Residue Count: 8,952
Deposited Residue Count: 11,969
Unique protein chains: 8

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G1-ATPase subunit beta	A, B, C, H, I A, B, C, H, I, J	784	Mycoplasma mobile 163K	Mutation(s): 0 EC: 3.6.3.14
UniProt
Find proteins for Q6KIC3 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711)) Explore Q6KIC3 Go to UniProtKB: Q6KIC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6KIC3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G1-ATPase subunit alpha	D, E, F, K, L D, E, F, K, L, M	528	Mycoplasma mobile 163K	Mutation(s): 0 EC: 3.6.3.14
UniProt
Find proteins for Q6KIC4 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711)) Explore Q6KIC4 Go to UniProtKB: Q6KIC4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6KIC4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
G1-ATPase subunit gamma	G, N	336	Mycoplasma mobile 163K	Mutation(s): 0
UniProt
Find proteins for Q6KIC7 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711)) Explore Q6KIC7 Go to UniProtKB: Q6KIC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6KIC7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	O, P, Q	511	Mycoplasma mobile 163K	Mutation(s): 0 EC: 2.7.2.3
UniProt
Find proteins for Q6KHJ1 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711)) Explore Q6KHJ1 Go to UniProtKB: Q6KHJ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6KHJ1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
G1-ATPase subunit D	R, S, T, U, V R, S, T, U, V, W	293	Mycoplasma mobile 163K	Mutation(s): 0
UniProt
Find proteins for Q6KIC8 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711)) Explore Q6KIC8 Go to UniProtKB: Q6KIC8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6KIC8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
G1-ATPase subunit E	X	112	Mycoplasma mobile 163K	Mutation(s): 0
UniProt
Find proteins for Q6KHS6 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711)) Explore Q6KHS6 Go to UniProtKB: Q6KHS6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6KHS6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
UNKNOWN HELIX	Y	13	Mycoplasma mobile 163K	Mutation(s): 0

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
UNKNOWN HELIX	Z	9	Mycoplasma mobile 163K	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain UA [auth M] SDF format, chain SA [auth L] SDF format, chain QA [auth K] SDF format, chain LA [auth H] SDF format, chain JA [auth F] SDF format, chain HA [auth E] SDF format, chain FA [auth D] SDF format, chain AA [auth A] MOL2 format, chain UA [auth M] MOL2 format, chain SA [auth L] MOL2 format, chain QA [auth K] MOL2 format, chain LA [auth H] MOL2 format, chain JA [auth F] MOL2 format, chain HA [auth E] MOL2 format, chain FA [auth D] MOL2 format, chain AA [auth A] mmCIF format, chain UA [auth M] mmCIF format, chain SA [auth L] mmCIF format, chain QA [auth K] mmCIF format, chain LA [auth H] mmCIF format, chain JA [auth F] mmCIF format, chain HA [auth E] mmCIF format, chain FA [auth D] mmCIF format, chain AA [auth A]	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		Interactions Focus chain AA [auth A] Focus chain FA [auth D] Focus chain HA [auth E] Focus chain JA [auth F] Focus chain LA [auth H] Focus chain QA [auth K] Focus chain SA [auth L] Focus chain UA [auth M] Interactions & Density Focus chain AA [auth A] Focus chain FA [auth D] Focus chain HA [auth E] Focus chain JA [auth F] Focus chain LA [auth H] Focus chain QA [auth K] Focus chain SA [auth L] Focus chain UA [auth M]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain OA [auth I] SDF format, chain DA [auth B] MOL2 format, chain OA [auth I] MOL2 format, chain DA [auth B] mmCIF format, chain OA [auth I] mmCIF format, chain DA [auth B]	DA [auth B], OA [auth I]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain DA [auth B] Focus chain OA [auth I] Interactions & Density Focus chain DA [auth B] Focus chain OA [auth I]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain PA [auth I] SDF format, chain EA [auth B] MOL2 format, chain PA [auth I] MOL2 format, chain EA [auth B] mmCIF format, chain PA [auth I] mmCIF format, chain EA [auth B]	EA [auth B], PA [auth I]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain EA [auth B] Focus chain PA [auth I] Interactions & Density Focus chain EA [auth B] Focus chain PA [auth I]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain VA [auth M] SDF format, chain TA [auth L] SDF format, chain RA [auth K] SDF format, chain NA [auth I] SDF format, chain MA [auth H] SDF format, chain KA [auth F] SDF format, chain IA [auth E] SDF format, chain GA [auth D] SDF format, chain CA [auth B] SDF format, chain BA [auth A] MOL2 format, chain VA [auth M] MOL2 format, chain TA [auth L] MOL2 format, chain RA [auth K] MOL2 format, chain NA [auth I] MOL2 format, chain MA [auth H] MOL2 format, chain KA [auth F] MOL2 format, chain IA [auth E] MOL2 format, chain GA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth A] mmCIF format, chain VA [auth M] mmCIF format, chain TA [auth L] mmCIF format, chain RA [auth K] mmCIF format, chain NA [auth I] mmCIF format, chain MA [auth H] mmCIF format, chain KA [auth F] mmCIF format, chain IA [auth E] mmCIF format, chain GA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth A]	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		Interactions Focus chain BA [auth A] Focus chain CA [auth B] Focus chain GA [auth D] Focus chain IA [auth E] Focus chain KA [auth F] Focus chain MA [auth H] Focus chain NA [auth I] Focus chain RA [auth K] Focus chain TA [auth L] Focus chain VA [auth M] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth B] Focus chain GA [auth D] Focus chain IA [auth E] Focus chain KA [auth F] Focus chain MA [auth H] Focus chain NA [auth I] Focus chain RA [auth K] Focus chain TA [auth L] Focus chain VA [auth M]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19
RECONSTRUCTION	cryoSPARC	3.3.2
RECONSTRUCTION	RELION	4.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP17H01544
Japan Science and Technology	Japan	JPMJCR19S5
Japan Agency for Medical Research and Development (AMED)	Japan	JP22am121003
Other government		--