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- EMDB-37637: Structural basis for the nucleosome binding and chromatin compact... -

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Entry
Database: EMDB / ID: EMD-37637
TitleStructural basis for the nucleosome binding and chromatin compaction by the linker histone H5
Map dataGlobular domain of linker histone H5 bound to mono-nucleosome with 177 bp DNA.
Sample
  • Complex: The complex of the H5 globular domain binding to the mono-nucleosome.
    • Complex: Histone H5
    • Complex: Core Histones
    • Complex: 601 DNA
KeywordsChromatin Fiber / Histone / DNA / Linker Histone / Nucleosome / Epigenetics / Genome Folding / Interaction / GENE REGULATION
Biological speciesGallus gallus (chicken) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi WY / Song F / Zhu P
Funding support China, United States, 10 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1300100 China
National Natural Science Foundation of China (NSFC)31991161 China
National Natural Science Foundation of China (NSFC)32230020 China
National Natural Science Foundation of China (NSFC)32241029 China
National Natural Science Foundation of China (NSFC)31730023 China
National Natural Science Foundation of China (NSFC)31500606 China
National Natural Science Foundation of China (NSFC)62131004 China
Chinese Academy of SciencesXDB37010100 China
Howard Hughes Medical Institute (HHMI)55008737 United States
Chinese Academy of Sciences153311KYSB20170020 China
CitationJournal: Cell Res / Year: 2024
Title: Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction.
Authors: Wenyan Li / Jie Hu / Feng Song / Juan Yu / Xin Peng / Shuming Zhang / Lin Wang / Mingli Hu / Jia-Cheng Liu / Yu Wei / Xue Xiao / Yan Li / Dongyu Li / Hui Wang / Bing-Rui Zhou / Linchang Dai ...Authors: Wenyan Li / Jie Hu / Feng Song / Juan Yu / Xin Peng / Shuming Zhang / Lin Wang / Mingli Hu / Jia-Cheng Liu / Yu Wei / Xue Xiao / Yan Li / Dongyu Li / Hui Wang / Bing-Rui Zhou / Linchang Dai / Zongjun Mou / Min Zhou / Haonan Zhang / Zheng Zhou / Huidong Zhang / Yawen Bai / Jin-Qiu Zhou / Wei Li / Guohong Li / Ping Zhu /
Abstract: The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order ...The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin fiber play a crucial role in biological processes related to DNA. Here, we report a 3.6-angstrom resolution cryogenic electron microscopy structure of H5-bound dodecanucleosome, i.e., the chromatin fiber reconstituted in the presence of linker histone H5, which shows a two-start left-handed double helical structure twisted by tetranucleosomal units. An atomic structural model of the H5-bound chromatin fiber, including an intact chromatosome, is built, which provides structural details of the full-length linker histone H5, including its N-terminal domain and an HMG-motif-like C-terminal domain. The chromatosome structure shows that H5 binds the nucleosome off-dyad through a three-contact mode in the chromatin fiber. More importantly, the H5-chromatin structure provides a fine molecular basis for the intra-tetranucleosomal and inter-tetranucleosomal interactions. In addition, we systematically validated the physiological functions and structural characteristics of the tetranucleosomal unit through a series of genetic and genomic studies in Saccharomyces cerevisiae and in vitro biophysical experiments. Furthermore, our structure reveals that multiple structural asymmetries of histone tails confer a polarity to the chromatin fiber. These findings provide structural and mechanistic insights into how a nucleosomal array folds into a higher-order chromatin fiber with a polarity in vitro and in vivo.
History
DepositionOct 2, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37637.png

Downloads & links

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Map

FileDownload / File: emd_37637.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobular domain of linker histone H5 bound to mono-nucleosome with 177 bp DNA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 228 pix.
= 237.12 Å		1.04 Å/pix.
x 228 pix.
= 237.12 Å		1.04 Å/pix.
x 228 pix.
= 237.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.268
Minimum - Maximum-1.125234 - 2.0012674
Average (Standard dev.)0.0036521642 (±0.073950335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions228228228
Spacing228228228
CellA=B=C: 237.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2.

Fileemd_37637_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_37637_half_map_2.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of the H5 globular domain binding to the mono-nucleosome.

EntireName: The complex of the H5 globular domain binding to the mono-nucleosome.
Components
  • Complex: The complex of the H5 globular domain binding to the mono-nucleosome.
    • Complex: Histone H5
    • Complex: Core Histones
    • Complex: 601 DNA

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Supramolecule #1: The complex of the H5 globular domain binding to the mono-nucleosome.

SupramoleculeName: The complex of the H5 globular domain binding to the mono-nucleosome.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1

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Supramolecule #2: Histone H5

SupramoleculeName: Histone H5 / type: complex / ID: 2 / Parent: 1 / Details: Globular domain of histone H5.
Source (natural)Organism: Gallus gallus (chicken)

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Supramolecule #3: Core Histones

SupramoleculeName: Core Histones / type: complex / ID: 3 / Parent: 1 / Details: Octameric core histones H2A, H2B, H3 and H4.
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #4: 601 DNA

SupramoleculeName: 601 DNA / type: complex / ID: 4 / Parent: 1 / Details: 12x177 bp tandem repeats of the Widom 601 DNA.
Source (natural)Organism: synthetic construct (others)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2nqb

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45705
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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