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- EMDB-65855: In situ subtomogram average of Hodarchaeales HC1 actin filament -

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Basic information

Entry
Database: EMDB / ID: EMD-65855
TitleIn situ subtomogram average of Hodarchaeales HC1 actin filament
Map dataHC1 actin filament
Sample
  • Organelle or cellular component: HC1 actin filament
    • Protein or peptide: HC1 actin
KeywordsAsgard archaea actin homolog Hodarchaeales In situ subtomogram average / PROTEIN FIBRIL
Biological speciesCandidatus Heimdallarchaeota archaeon (archaea) / Candidatus Hodarchaeales (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 19.8 Å
AuthorsImachi H / Nobu MK / Ishii S / Hashiguchi H / Hirakata Y / Hosogi N / Ikuta T / Isaji Y / Miyata M / Miyazaki M ...Imachi H / Nobu MK / 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 YO / Takaki Y / Takano Y / Tasumi E / Uematsu K / Yoshimura T / Takai K
Funding support Japan, 10 items
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 MK / 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 ...Authors: Imachi H / Nobu MK / 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 YO / Takaki Y / Takano Y / Tasumi E / Uematsu K / Yoshimura T / Takai K
History
DepositionAug 15, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65855.png

Downloads & links

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Map

FileDownload / File: emd_65855.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHC1 actin filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.19 Å/pix.
x 64 pix.
= 396.288 Å		6.19 Å/pix.
x 64 pix.
= 396.288 Å		6.19 Å/pix.
x 64 pix.
= 396.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.192 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 100.0
Minimum - Maximum-128.247199999999992 - 218.420600000000007
Average (Standard dev.)1.6010619 (±23.193819999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 396.288 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_65855_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_65855_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HC1 actin filament

EntireName: HC1 actin filament
Components
  • Organelle or cellular component: HC1 actin filament
    • Protein or peptide: HC1 actin

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Supramolecule #1: HC1 actin filament

SupramoleculeName: HC1 actin filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea) / Strain: HC1

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Macromolecule #1: HC1 actin

MacromoleculeName: HC1 actin / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Hodarchaeales (archaea) / Strain: HC1
Molecular weightTheoretical: 45.307977 KDa
SequenceString: MRWIHPEQLT IAIALEKHPK VVKMSEEASG KPLVVDNGTG LSKNGYAGED QPRTVFPSLV GYPKYQGIMS DVDHYVREYY VGEEAMNLR GVLKLMYPIE HGTVSDWDAM EKIWHYTFHN DLRVNPADHP VLLTEPPMNP ESNKLKMAEI LFETFNVPAF H VSMQAVLS ...String:
MRWIHPEQLT IAIALEKHPK VVKMSEEASG KPLVVDNGTG LSKNGYAGED QPRTVFPSLV GYPKYQGIMS DVDHYVREYY VGEEAMNLR GVLKLMYPIE HGTVSDWDAM EKIWHYTFHN DLRVNPADHP VLLTEPPMNP ESNKLKMAEI LFETFNVPAF H VSMQAVLS LYASGRTTGL VVDAGDGVVH IVPIYEGFSV SHAIRRIDLA GRDLTAHLQK LLMARGHKFV SSAEKEIVRD IK ERLCYVA LEPEKELKLA EKHQGMEKQY ILPDGQTITV GVERFKAPEA LFNPAMVGKE DDPLDDAIFG AVQACDIDLR KEL YQNIVL SGGTTMFPGL KERLHKELTE LVPENVEIRI VAPPERRYSV WIGGSILASL KTFQRLWISK NEYQESGGQA IKRL GF

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil Active R2/1 / Material: MOLYBDENUM / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 9.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 19500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 31.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -168.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 19.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 1491
ExtractionNumber tomograms: 1 / Number images used: 10247
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9wc4:
Hodarchaeales HC1 actin filament

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