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- EMDB-9640: 112-bp octasome/DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9640
Title112-bp octasome/DNA complex
Map data
Sample
  • Complex: 112-bp octasome/DNA complex
    • Complex: Histone H2A
    • Complex: Histone H2B
    • Complex: Histone H3.1
    • Complex: Histone H4
    • Complex: 112bp 601 DNA
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsMayanagi K / Saikusa K / Miyazaki N / Akashi S / Iwasaki K / Nishimura Y / Morikawa K / Tsunaka Y
Funding support Japan, 11 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am0101073 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101072j0001 Japan
Japan Society for the Promotion of ScienceJP26251008 Japan
Japan Society for the Promotion of ScienceJP16K18528 Japan
Japan Society for the Promotion of ScienceJP16H01410 Japan
Japan Society for the Promotion of ScienceJP17K07313 Japan
Japan Society for the Promotion of Science18K06089 Japan
Japan Society for the Promotion of ScienceJP18K06064 Japan
Japan Society for the Promotion of ScienceJP26505009 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101076 Japan
Japan Science and TechnologyJPMJPR12L9 Japan
CitationJournal: Genes Dev / Year: 2016
Title: Integrated molecular mechanism directing nucleosome reorganization by human FACT.
Authors: Yasuo Tsunaka / Yoshie Fujiwara / Takuji Oyama / Susumu Hirose / Kosuke Morikawa /
Abstract: Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT- ...Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT-histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3-H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular β structure with H4. At the other site, the Mid-H2A steric collision on the H2A-docking surface of the H3-H4 tetramer within the nucleosome induces H2A-H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone.
History
DepositionAug 29, 2018-
Header (metadata) releaseJul 31, 2019-
Map releaseJul 31, 2019-
UpdateJul 31, 2019-
Current statusJul 31, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.125
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9640.png

Downloads & links

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Map

FileDownload / File: emd_9640.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 128 pix.
= 179.2 Å		1.4 Å/pix.
x 128 pix.
= 179.2 Å		1.4 Å/pix.
x 128 pix.
= 179.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125 / Movie #1: 0.125
Minimum - Maximum-0.3247932 - 0.49800757
Average (Standard dev.)0.005142457 (±0.034249816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 179.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z179.200179.200179.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.3250.4980.005

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Supplemental data

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Sample components

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Entire : 112-bp octasome/DNA complex

EntireName: 112-bp octasome/DNA complex
Components
  • Complex: 112-bp octasome/DNA complex
    • Complex: Histone H2A
    • Complex: Histone H2B
    • Complex: Histone H3.1
    • Complex: Histone H4
    • Complex: 112bp 601 DNA

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Supramolecule #1: 112-bp octasome/DNA complex

SupramoleculeName: 112-bp octasome/DNA complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3)
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: Histone H2A

SupramoleculeName: Histone H2A / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3)

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Supramolecule #3: Histone H2B

SupramoleculeName: Histone H2B / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3)

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Supramolecule #4: Histone H3.1

SupramoleculeName: Histone H3.1 / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3)

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Supramolecule #5: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3)

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Supramolecule #6: 112bp 601 DNA

SupramoleculeName: 112bp 601 DNA / type: complex / ID: 6 / Parent: 1
Details: 112 bp fragment of Widom-601 strong nucleosome positioning DNA sequence
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria) / Recombinant strain: DH5[alpha]

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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

Concentration2.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 20 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 37441
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
FSC plot (resolution estimation)

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