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- PDB-9wc4: Hodarchaeales HC1 actin filament -

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Basic information

Entry
Database: PDB / ID: 9wc4
TitleHodarchaeales HC1 actin filament
ComponentsHC1 actin
KeywordsPROTEIN FIBRIL / Asgard archaea actin homolog Hodarchaeales In situ subtomogram average
Biological speciesCandidatus Hodarchaeales (archaea)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 19.8 Å
AuthorsImachi, H. / Nobu, M.K. / Ishii, S. / Hashiguchi, H. / Hirakata, Y. / Hosogi, N. / Ikuta, T. / Isaji, Y. / Miyata, M. / Miyazaki, M. ...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 support Japan, 10items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H01005 Japan
Japan Society for the Promotion of Science (JSPS)22H04985 Japan
Japan Society for the Promotion of Science (JSPS)24H00582 Japan
Japan Society for the Promotion of Science (JSPS)22H04926 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121005 Japan
Japan Society for the Promotion of Science (JSPS)23K27145 Japan
Other government23NIPS201
Other government24NIPS201
Other governmentGBMF9743
Other governmentL-2024-1-003
CitationJournal: To Be Published
Title: Eukaryotes' closest relatives are internally simple syntrophic archaea
Authors: 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. / ...Authors: 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.
History
DepositionAug 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HC1 actin
B: HC1 actin
C: HC1 actin
E: HC1 actin
F: HC1 actin
G: HC1 actin
D: HC1 actin


Theoretical massNumber of molelcules
Total (without water)317,1567
Polymers317,1567
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
HC1 actin


Mass: 45307.977 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Candidatus Hodarchaeales (archaea) / Strain: HC1
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: HC1 actin filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea) / Strain: HC1
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid type: Quantifoil Active R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 19500 X / Nominal defocus max: 9000 nm / Nominal defocus min: 8000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.5 e/Å2 / Avg electron dose per subtomogram: 85 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 5 eV

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Processing

EM software
IDNameVersionCategory
4RELION4CTF correction
10RELION4final Euler assignment
12RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -168.4 ° / Axial rise/subunit: 31.4 Å / Axial symmetry: C1
3D reconstructionResolution: 19.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1491 / Symmetry type: HELICAL
EM volume selectionNum. of tomograms: 1 / Num. of volumes extracted: 10247
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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