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- EMDB-23404: Reconsituted 207 bp Archaeasome, Class II -

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Basic information

Entry
Database: EMDB / ID: EMD-23404
TitleReconsituted 207 bp Archaeasome, Class II
Map dataReconstructed density of the Arc207 archaeasome complex. 7 histone dimers wrap 207 bp of DNA through a 4 dimer (Arc120) "base" and 3 dimer (Arc90) "lid" arrangement.
Sample
  • Complex: Archaeasome containing 207 bp of DNA
Biological speciesThermococcus kodakarensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsBowerman S / Luger K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM137496 United States
CitationJournal: Elife / Year: 2021
Title: Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways.
Authors: Samuel Bowerman / Jeff Wereszczynski / Karolin Luger /
Abstract: Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form 'nucleosome-like' complexes that ...Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form 'nucleosome-like' complexes that continuously wind between 60 and 500 base pairs of DNA ('archaeasomes'), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90 out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility.
History
DepositionFeb 2, 2021-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.163
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.163
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23404.png

Downloads & links

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Map

FileDownload / File: emd_23404.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstructed density of the Arc207 archaeasome complex. 7 histone dimers wrap 207 bp of DNA through a 4 dimer (Arc120) "base" and 3 dimer (Arc90) "lid" arrangement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 256 pix.
= 312.064 Å		1.22 Å/pix.
x 256 pix.
= 312.064 Å		1.22 Å/pix.
x 256 pix.
= 312.064 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.219 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.163 / Movie #1: 0.163
Minimum - Maximum-0.124475926 - 0.52195036
Average (Standard dev.)0.0023662183 (±0.03629396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 312.064 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2191.2191.219
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z312.064312.064312.064
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ416416416
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1240.5220.002

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Supplemental data

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Sample components

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Entire : Archaeasome containing 207 bp of DNA

EntireName: Archaeasome containing 207 bp of DNA
Components
  • Complex: Archaeasome containing 207 bp of DNA

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Supramolecule #1: Archaeasome containing 207 bp of DNA

SupramoleculeName: Archaeasome containing 207 bp of DNA / type: complex / ID: 1 / Parent: 0
Details: Archaeasome (archaeal histone-DNA complex) formed by 7 histone dimers wrapping 207 bp of DNA.
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMKClPotassium chloride
50.0 mMTris-HCltris(hydroxymethyl)aminomethane hydrochloride
GridModel: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE / Details: 40 mA
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Manual plunge at ambient temperature and humidity..
DetailsSample was observed to be monodisperse via Sedimentation Velocity Analytical Ultracentrifugation.

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5388 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD

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Image processing

Particle selectionNumber selected: 1879294
Details: Particles selected using crYOLO, manual training sets constructed from JANNI-denoised micrographs.
CTF correctionSoftware - Name: Gctf
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Number images used: 5959
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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