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- EMDB-6838: Nucleosome with ALB1 enhancer DNA sequence -

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Basic information

Entry
Database: EMDB / ID: EMD-6838
TitleNucleosome with ALB1 enhancer DNA sequence
Map data
SampleNucleosome with ALB1-DNA sequence
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / DNA replication-independent nucleosome assembly / telomere capping / telomere organization / DNA replication-dependent nucleosome assembly / nuclear nucleosome / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing by miRNA ...negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / DNA replication-independent nucleosome assembly / telomere capping / telomere organization / DNA replication-dependent nucleosome assembly / nuclear nucleosome / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing by miRNA / nuclear chromosome / DNA-templated transcription, initiation / regulation of megakaryocyte differentiation / nucleosome assembly / nucleosome / double-strand break repair via nonhomologous end joining / nuclear chromosome, telomeric region / protein heterodimerization activity / protein domain specific binding / cellular protein metabolic process / host cell nucleus / protein-containing complex / RNA binding / DNA binding / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus
Histone H4, conserved site / CENP-T/Histone H4, histone fold / Histone-fold / TATA box binding protein associated factor (TAF) / Histone H4
Histone H4
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsTakizawa Y / Tanaka H / Machida S / Koyama M / Maehara K / Ohkawa Y / Wade PA / Wolf M / Kurumizaka H
CitationJournal: Open Biol / Year: 2018
Title: Cryo-EM structure of the nucleosome containing the enhancer DNA sequence.
Authors: Yoshimasa Takizawa / Hiroki Tanaka / Shinichi Machida / Masako Koyama / Kazumitsu Maehara / Yasuyuki Ohkawa / Paul A Wade / Matthias Wolf / Hitoshi Kurumizaka /
Abstract: Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the gene enhancer in liver precursor ...Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the enhancer (N1) sequence, by cryogenic electron microscopy at 4.0 Å resolution. The nucleosome structure with the enhancer DNA is not significantly different from the previously reported nucleosome structure with the Widom 601 DNA. Interestingly, in the nucleosomes, the enhancer DNA contains local flexible regions, as compared to the Widom 601 DNA. Consistently, DNaseI treatments revealed that, in the nucleosome, the enhancer (N1) DNA is more accessible than the Widom 601 sequence. The histones also associated less strongly with the enhancer (N1) DNA than the Widom 601 DNA in the nucleosome. Therefore, the local histone-DNA contacts may be responsible for the enhanced DNA accessibility in the nucleosome with the enhancer DNA.
History
DepositionOct 18, 2017-
Header (metadata) releaseApr 11, 2018-
Map releaseApr 11, 2018-
UpdateApr 11, 2018-
Current statusApr 11, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6838.map.gz / Format: CCP4 / Size: 10.5 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 140 pix.
= 196. Å
1.4 Å/pix.
x 140 pix.
= 196. Å
1.4 Å/pix.
x 140 pix.
= 196. 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
Contour LevelBy AUTHOR: 5.4 / Movie #1: 5.4
Minimum - Maximum-10.054035000000001 - 19.075044999999999
Average (Standard dev.)-0.000000006212297 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 196.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z196.000196.000196.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-10.05419.075-0.000

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Supplemental data

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Sample components

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Entire Nucleosome with ALB1-DNA sequence

EntireName: Nucleosome with ALB1-DNA sequence / Number of components: 1

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Component #1: protein, Nucleosome with ALB1-DNA sequence

ProteinName: Nucleosome with ALB1-DNA sequence / Recombinant expression: No
MassTheoretical: 200 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)
Vector: pET15b-H3.1, pET15b-H4, pET15b-H2A, pET15b-H2B, pGEM-T-Easy-(186 base-pair mouse ALB1 enhancer DNA)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.8 mg/mL / pH: 7.5
Support filmGatan Solarus
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 289 K / Humidity: 100 % / Details: 3 second blot, 2.5uL.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA / Details: nanoprobe, parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 80 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 73000.0 X (nominal), 100000.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1500.0 - -3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (77.0 - 100.0 K)
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2312 / Sampling size: 14 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 288789
Details: frame alignment and integration with motioncor2 incl. dose weighting
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / CTF correction: deconvolution in RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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