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- EMDB-40030: Hir1 WD40 domains and Asf1/H3/H4 -

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Basic information

Entry
Database: EMDB / ID: EMD-40030
TitleHir1 WD40 domains and Asf1/H3/H4
Map data
Sample
  • Complex: Hir1 WD40 domains and Asf1/H3/H4
    • Complex: Hir1 WD40 with Hpc2
    • Complex: Asf1/H3/H4
KeywordsHistone / Complex / Replication-Independent / CHAPERONE
Function / homology
Function and homology information


negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA replication-dependent chromatin assembly / nucleosome disassembly / rRNA transcription / chromosome, centromeric region / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle ...negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA replication-dependent chromatin assembly / nucleosome disassembly / rRNA transcription / chromosome, centromeric region / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / chromatin organization / chromosome / histone binding / chromatin remodeling / protein heterodimerization activity / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus
Similarity search - Function
Hpc2-related domain / HIRA B motif / HPC2 and ubinuclein domain / HIRA B motif / TUP1-like enhancer of split / WD repeat HIR1 / Histone transcription regulator 3/CABIN1 / TUP1-like enhancer of split / Histone deposition protein Asf1 / Histone chaperone ASF1-like ...Hpc2-related domain / HIRA B motif / HPC2 and ubinuclein domain / HIRA B motif / TUP1-like enhancer of split / WD repeat HIR1 / Histone transcription regulator 3/CABIN1 / TUP1-like enhancer of split / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H4 / Histone H3 / Histone chaperone / Protein HIR1 / Histone transcription regulator 3 / Histone promoter control protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsKim HJ / Murakami K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123233 United States
CitationJournal: Mol Cell / Year: 2024
Title: Structure of the Hir histone chaperone complex.
Authors: Hee Jong Kim / Mary R Szurgot / Trevor van Eeuwen / M Daniel Ricketts / Pratik Basnet / Athena L Zhang / Austin Vogt / Samah Sharmin / Craig D Kaplan / Benjamin A Garcia / Ronen Marmorstein / Kenji Murakami /
Abstract: The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1a/Asf1 co-chaperone cooperate to deposit histone (H3/H4) tetramers on DNA for replication-independent chromatin assembly. The ...The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1a/Asf1 co-chaperone cooperate to deposit histone (H3/H4) tetramers on DNA for replication-independent chromatin assembly. The molecular architecture of the HIRA/Hir complex and its mode of histone deposition have remained unknown. Here, we report the cryo-EM structure of the S. cerevisiae Hir complex with Asf1/H3/H4 at 2.9-6.8 Å resolution. We find that the Hir complex forms an arc-shaped dimer with a Hir1/Hir2/Hir3/Hpc2 stoichiometry of 2/4/2/4. The core of the complex containing two Hir1/Hir2/Hir2 trimers and N-terminal segments of Hir3 forms a central cavity containing two copies of Hpc2, with one engaged by Asf1/H3/H4, in a suitable position to accommodate a histone (H3/H4) tetramer, while the C-terminal segments of Hir3 harbor nucleic acid binding activity to wrap DNA around the Hpc2-assisted histone tetramer. The structure suggests a model for how the Hir/Asf1 complex promotes the formation of histone tetramers for their subsequent deposition onto DNA.
History
DepositionMar 9, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40030.png

Downloads & links

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Map

FileDownload / File: emd_40030.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0077
Minimum - Maximum-0.011533851 - 0.03986129
Average (Standard dev.)0.00006600955 (±0.0013769491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40030_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_40030_half_map_2.map
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Sample components

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Entire : Hir1 WD40 domains and Asf1/H3/H4

EntireName: Hir1 WD40 domains and Asf1/H3/H4
Components
  • Complex: Hir1 WD40 domains and Asf1/H3/H4
    • Complex: Hir1 WD40 with Hpc2
    • Complex: Asf1/H3/H4

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Supramolecule #1: Hir1 WD40 domains and Asf1/H3/H4

SupramoleculeName: Hir1 WD40 domains and Asf1/H3/H4 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #2: Hir1 WD40 with Hpc2

SupramoleculeName: Hir1 WD40 with Hpc2 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Asf1/H3/H4

SupramoleculeName: Asf1/H3/H4 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: ab initio modeling from curated 2D classified particles
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326671
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ghm:
Hir1 WD40 domains and Asf1/H3/H4

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