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- EMDB-2602: Cryo-EM study of the chromatin fiber reveals a double helix twist... -

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Basic information

Entry
Database: EMDB / ID: EMD-2602
TitleCryo-EM study of the chromatin fiber reveals a double helix twisted by tetra-nucleosomal units
Map dataReconstruction of 24x177 bp chromatin
Sample
  • Sample: In vitro reconstituted 24x177 bp chromatin
  • Protein or peptide: Core histone
  • Protein or peptide: Histone H1.4
  • DNA: 601 DNA
KeywordsIn vitro reconstituted 24x177 bp chromatin
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsSong F / Chen P / Sun D / Wang M / Dong L / Liang D / Xu RM / Zhu P / Li G
CitationJournal: Science / Year: 2014
Title: Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.
Authors: Feng Song / Ping Chen / Dapeng Sun / Mingzhu Wang / Liping Dong / Dan Liang / Rui-Ming Xu / Ping Zhu / Guohong Li /
Abstract: The hierarchical packaging of eukaryotic chromatin plays a central role in transcriptional regulation and other DNA-related biological processes. Here, we report the 11-angstrom-resolution cryogenic ...The hierarchical packaging of eukaryotic chromatin plays a central role in transcriptional regulation and other DNA-related biological processes. Here, we report the 11-angstrom-resolution cryogenic electron microscopy (cryo-EM) structures of 30-nanometer chromatin fibers reconstituted in the presence of linker histone H1 and with different nucleosome repeat lengths. The structures show a histone H1-dependent left-handed twist of the repeating tetranucleosomal structural units, within which the four nucleosomes zigzag back and forth with a straight linker DNA. The asymmetric binding and the location of histone H1 in chromatin play a role in the formation of the 30-nanometer fiber. Our results provide mechanistic insights into how nucleosomes compact into higher-order chromatin fibers.
History
DepositionMar 5, 2014-
Header (metadata) releaseApr 9, 2014-
Map releaseMay 7, 2014-
UpdateMay 7, 2014-
Current statusMay 7, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.496
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.496
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2602.png

emd_2602_1.png

Downloads & links

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Map

FileDownload / File: emd_2602.map.gz / Format: CCP4 / Size: 268.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of 24x177 bp chromatin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 416 pix.
= 739.648 Å		1.78 Å/pix.
x 416 pix.
= 739.648 Å		1.78 Å/pix.
x 416 pix.
= 739.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.496 / Movie #1: 0.496
Minimum - Maximum-0.67342383 - 2.66036606
Average (Standard dev.)0.01618698 (±0.17536815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208-208-208
Dimensions416416416
Spacing416416416
CellA=B=C: 739.648 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7781.7781.778
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z739.648739.648739.648
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-208-208-208
NC/NR/NS416416416
D min/max/mean-0.6732.6600.016

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Supplemental data

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Sample components

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Entire : In vitro reconstituted 24x177 bp chromatin

EntireName: In vitro reconstituted 24x177 bp chromatin
Components
  • Sample: In vitro reconstituted 24x177 bp chromatin
  • Protein or peptide: Core histone
  • Protein or peptide: Histone H1.4
  • DNA: 601 DNA

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Supramolecule #1000: In vitro reconstituted 24x177 bp chromatin

SupramoleculeName: In vitro reconstituted 24x177 bp chromatin / type: sample / ID: 1000 / Oligomeric state: Didodecamer / Number unique components: 3

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Macromolecule #1: Core histone

MacromoleculeName: Core histone / type: protein_or_peptide / ID: 1
Details: Octameric nucleosome core histone contains 2 copies histone H2A, H2B, H3 and H4. 12 octamer units constitutes the twenty-four-mer.
Number of copies: 2 / Oligomeric state: Octamer / Recombinant expression: Yes
Source (natural)Organism: Xenopus laevis (African clawed frog) / Location in cell: Nucleus
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #2: Histone H1.4

MacromoleculeName: Histone H1.4 / type: protein_or_peptide / ID: 2 / Name.synonym: HISTIHIE
Details: Each octamer contains 1 copy linker histone, histone H1.4
Number of copies: 24 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #3: 601 DNA

MacromoleculeName: 601 DNA / type: dna / ID: 3 / Details: 24 tandem repeats; full length 4248 bp / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: unidentified (others)
SequenceString:
GAGCATCCGG ATCCCCTGGA GAATCCCGGT GCCGAGGCCG CTCAATTGGT CGTAGACAGC TCTAGCACCG CTTAAACGCA CGTACGCGCT GTCCCCCGCG TTTTAACCGC CAAGGGGATT ACTCCCTAGT CTCCAGGCAC GTGTCACATA TATACATCCT GTTCCAGTGC CGGACCC

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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

BufferpH: 8 / Details: 10 mM HEPES, pH 8.0, 0.1 mM EDTA
GridDetails: 300 mesh R2.1 Quantifoil holey grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: Sample absorbed for 1 to 1.5 min, blotted for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 155,000 times magnification
DetailsParallel beam illumination
DateNov 1, 2013
Image recordingCategory: CCD / Film or detector model: OTHER / Average electron dose: 18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.75 µm / Nominal defocus min: 2.23 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF correction of each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 5000

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