[English] 日本語
Yorodumi
- EMDB-53386: Asgard Archaeal HHoB nucleosome in the closed conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53386
TitleAsgard Archaeal HHoB nucleosome in the closed conformation
Map dataHHoB Asgard nucleosome in the closed conformation
Sample
  • Complex: Closed complex of HHoB Asgard archaeal histone HHoB and DNA
    • Protein or peptide: Archaeal histone A
    • DNA: DNA (120-MER) part of a full 147 bp Widom601 DNA
    • DNA: DNA (120-MER) part of a full 147 bp Widom601 DNA
KeywordsArchaea / Asgard / chromatin / nucleosome / DNA BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesCandidatus Heimdallarchaeota archaeon LC_3 (archaea) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRanawat HM / Dodonova SO
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)3DchromArchaea 101076671European Union
CitationJournal: Mol.Cell / Year: 2025
Title: Cryo-EM reveals open and closed Asgard chromatin assemblies
Authors: Ranawat HM / Cajili MK / Lopez-Barbosa N / Quail T / Dame RT / Dodonova SO
History
DepositionApr 11, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53386.png

Downloads & links

-
Map

FileDownload / File: emd_53386.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHHoB Asgard nucleosome in the closed conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.37 Å/pix.
x 704 pix.
= 256.96 Å		0.37 Å/pix.
x 704 pix.
= 256.96 Å		0.37 Å/pix.
x 704 pix.
= 256.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.365 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0596885 - 0.09380742
Average (Standard dev.)0.000057502177 (±0.0017088207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions704704704
Spacing704704704
CellA=B=C: 256.96002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53386_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_53386_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_53386_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Closed complex of HHoB Asgard archaeal histone HHoB and DNA

EntireName: Closed complex of HHoB Asgard archaeal histone HHoB and DNA
Components
  • Complex: Closed complex of HHoB Asgard archaeal histone HHoB and DNA
    • Protein or peptide: Archaeal histone A
    • DNA: DNA (120-MER) part of a full 147 bp Widom601 DNA
    • DNA: DNA (120-MER) part of a full 147 bp Widom601 DNA

-
Supramolecule #1: Closed complex of HHoB Asgard archaeal histone HHoB and DNA

SupramoleculeName: Closed complex of HHoB Asgard archaeal histone HHoB and DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: in presence of 1mM Mg
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Molecular weightTheoretical: 137 KDa

-
Macromolecule #1: Archaeal histone A

MacromoleculeName: Archaeal histone A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Strain: LC_3
Molecular weightTheoretical: 7.524643 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGNFANARV EKLIRQAGAQ RVSADAVDKM NEILTDWGKN IAKYAVEIAR HSGRKTVKEN DIKLAAQK

UniProtKB: UNIPROTKB: A0A1Q9NRY6

-
Macromolecule #2: DNA (120-MER) part of a full 147 bp Widom601 DNA

MacromoleculeName: DNA (120-MER) part of a full 147 bp Widom601 DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 36.849469 KDa
SequenceString: (DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC) (DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA) (DC) (DC)(DG)(DC)(DT)(DT)(DA) ...String:
(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC) (DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA) (DC) (DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG) (DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC) (DG)(DC)(DC)(DA)(DA)(DG) (DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC) (DC)(DC)(DT)(DA) (DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG) (DT)(DC)(DA)(DG)(DA)

-
Macromolecule #3: DNA (120-MER) part of a full 147 bp Widom601 DNA

MacromoleculeName: DNA (120-MER) part of a full 147 bp Widom601 DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 37.218699 KDa
SequenceString: (DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG) (DC) (DG)(DG)(DT)(DT)(DA)(DA) ...String:
(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG) (DC) (DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC) (DA)(DG) (DC)(DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA) (DG)(DC)(DG) (DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC) (DG)(DG)(DC)(DA)(DC)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.192 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClSodium Chloride
1.0 mMMgCl2Magnesium Chloride

Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 1mM MgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: at 20* C.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Average electron dose: 59.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3108514
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction in cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Details: in cryosparc / Number images used: 117260
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Ab-initio reconstruction
Details: stochastic gradient descent (SGD), which optimizes particle poses by iteratively minimizing the alignment error.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Non-uniform refinement
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChainDetails

nry6

chain_id: A, residue_range: 1-68, source_name: AlphaFold, initial_model_type: in silico modelMonomer prediction of HHoB

1aoi

chain_id: I, residue_range: 1-120, source_name: PDB, initial_model_type: experimental modelDNA monomer

1aoi

chain_id: J, residue_range: 172-292, source_name: PDB, initial_model_type: experimental modelDNA monomer
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qv5:
Asgard Archaeal HHoB nucleosome in the closed conformation

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more