+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40037 | |||||||||
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Title | Composite map of the Hir complex with Asf1/H3/H4 | |||||||||
Map data | a composite map of the Hir with Asf1/H3/H4 | |||||||||
Sample |
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Keywords | Histone / 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) / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes ...negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / nucleosome disassembly / SUMOylation of chromatin organization proteins / transcription elongation-coupled chromatin remodeling / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / Estrogen-dependent gene expression / chromosome, centromeric region / intracellular copper ion homeostasis / CENP-A containing nucleosome / aerobic respiration / 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 / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Kim HJ / Murakami K | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40037.map.gz | 21.8 MB | EMDB map data format | |
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Header (meta data) | emd-40037-v30.xml emd-40037.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_40037.png | 74.9 KB | ||
Filedesc metadata | emd-40037.cif.gz | 3.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40037 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40037 | HTTPS FTP |
-Validation report
Summary document | emd_40037_validation.pdf.gz | 351.8 KB | Display | EMDB validaton report |
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Full document | emd_40037_full_validation.pdf.gz | 351.4 KB | Display | |
Data in XML | emd_40037_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | emd_40037_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40037 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40037 | HTTPS FTP |
-Related structure data
Related structure data | 8ghnMC 8ghaC 8ghlC 8ghmC 8gixC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40037.map.gz / Format: CCP4 / Size: 512.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | a composite map of the Hir with Asf1/H3/H4 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : the yeast Hir complex with Asf1/H3/H4
Entire | Name: the yeast Hir complex with Asf1/H3/H4 |
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Components |
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-Supramolecule #1: the yeast Hir complex with Asf1/H3/H4
Supramolecule | Name: the yeast Hir complex with Asf1/H3/H4 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 1.24 MDa |
-Supramolecule #2: the yeast Hir complex
Supramolecule | Name: the yeast Hir complex / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Supramolecule #3: Asf1/H3/H4
Supramolecule | Name: Asf1/H3/H4 / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 639000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |