+Open data
-Basic information
Entry | Database: PDB / ID: 8ghn | ||||||
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Title | Composite model of the yeast Hir Complex with Asf1/H3/H4 | ||||||
Components |
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Keywords | CHAPERONE / Histone / Complex / Replication-Independent | ||||||
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) / RNA polymerase I upstream activating factor complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression ...negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / RNA polymerase I upstream activating factor complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / 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 / DNA replication-dependent chromatin assembly / replication fork protection complex / Oxidative Stress Induced Senescence / prenyltransferase activity / nucleosome disassembly / isoprenoid biosynthetic process / 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 / Estrogen-dependent gene expression / rRNA transcription / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å | ||||||
Authors | Kim, H.J. / Murakami, K. | ||||||
Funding support | United States, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ghn.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ghn.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 8ghn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ghn_validation.pdf.gz | 888.1 KB | Display | wwPDB validaton report |
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Full document | 8ghn_full_validation.pdf.gz | 996 KB | Display | |
Data in XML | 8ghn_validation.xml.gz | 175.8 KB | Display | |
Data in CIF | 8ghn_validation.cif.gz | 272 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/8ghn ftp://data.pdbj.org/pub/pdb/validation_reports/gh/8ghn | HTTPS FTP |
-Related structure data
Related structure data | 40037MC 8ghaC 8ghlC 8ghmC 8gixC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 7 types, 15 molecules AGBCHIDJEFKLMNO
#1: Protein | Mass: 93983.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32479 #2: Protein | Mass: 98553.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32480 #3: Protein | Mass: 191915.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47171 #4: Protein | Mass: 67877.391 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01448 #5: Protein | | Mass: 15391.007 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / References: UniProt: P61830 #6: Protein | | Mass: 11395.390 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309 #7: Protein | | Mass: 31629.260 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ASF1, GI527_G0003133 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L0YDQ7 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 1.24 MDa / Experimental value: YES | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 639629 / Algorithm: FOURIER SPACE / Details: A composite map from Maps 1-3 / Symmetry type: POINT | ||||||||||||||||||||||||
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