9WC4 | pdb_00009wc4

Hodarchaeales HC1 actin filament

• PDB DOI: https://doi.org/10.2210/pdb9WC4/pdb
• EM Map EMD-65855: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Candidatus Hodarchaeales
• Mutation(s): No 


• Deposited: 2025-08-15 Released: 2026-06-24 
• Deposition Author(s): Imachi, H., Nobu, M.K., Ishii, S., Hashiguchi, H., Hirakata, Y., Hosogi, N., Ikuta, T., Isaji, Y., Miyata, M., Miyazaki, M., Morono, Y., Murata, K., Nakagawa, S., Narita, A., Ogawara, M., Okada, S., Saito, Y., Sakai, S., Shimamura, S., Tahara, Y.O., Takaki, Y., Takano, Y., Tasumi, E., Uematsu, K., Yoshimura, T., Takai, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 19.8 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: in silico

Literature

Eukaryotes' closest relatives are internally simple syntrophic archaea

Imachi, H., Nobu, M.K., Ishii, S., Hashiguchi, H., Hirakata, Y., Hosogi, N., Ikuta, T., Isaji, Y., Miyata, M., Miyazaki, M., Morono, Y., Murata, K., Nakagawa, S., Narita, A., Ogawara, M., Okada, S., Saito, Y., Sakai, S., Shimamura, S., Tahara, Y.O., Takaki, Y., Takano, Y., Tasumi, E., Uematsu, K., Yoshimura, T., Takai, K.

To be published.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 317.16 kDa 
• Atom Count: 22,309 
• Modeled Residue Count: 2,814 
• Deposited Residue Count: 2,814 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HC1 actin	A, B, C, D [auth E], E [auth F], F [auth G], G [auth D]	402	Candidatus Hodarchaeales	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 19.8 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-24 
Deposition Author(s): Imachi, H., Nobu, M.K., Ishii, S., Hashiguchi, H., Hirakata, Y., Hosogi, N., Ikuta, T., Isaji, Y., Miyata, M., Miyazaki, M., Morono, Y., Murata, K., Nakagawa, S., Narita, A., Ogawara, M., Okada, S., Saito, Y., Sakai, S., Shimamura, S., Tahara, Y.O., Takaki, Y., Takano, Y., Tasumi, E., Uematsu, K., Yoshimura, T., Takai, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H01005
Japan Society for the Promotion of Science (JSPS)	Japan	22H04985
Japan Society for the Promotion of Science (JSPS)	Japan	24H00582
Japan Society for the Promotion of Science (JSPS)	Japan	22H04926
Japan Agency for Medical Research and Development (AMED)	Japan	JP24ama121005
Japan Society for the Promotion of Science (JSPS)	Japan	23K27145
Other government		23NIPS201
Other government		24NIPS201
Other government		GBMF9743
Other government		L-2024-1-003

Revision History  

• Version 1.0: 2026-06-24
  Type: Initial release