+Open data
-Basic information
Entry | Database: PDB / ID: 8ghl | ||||||
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Title | the Hir complex core | ||||||
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) / transcription elongation-coupled chromatin remodeling / chromosome, centromeric region / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / transcription corepressor activity / nucleosome assembly ...negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / transcription elongation-coupled chromatin remodeling / chromosome, centromeric region / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / transcription corepressor activity / nucleosome assembly / chromatin organization / chromosome / chromatin remodeling / chromatin / negative regulation of transcription by RNA polymerase II / 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 | 8ghl.cif.gz | 743 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ghl.ent.gz | 567.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ghl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ghl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ghl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8ghl_validation.xml.gz | 102.3 KB | Display | |
Data in CIF | 8ghl_validation.cif.gz | 160.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/8ghl ftp://data.pdbj.org/pub/pdb/validation_reports/gh/8ghl | HTTPS FTP |
-Related structure data
Related structure data | 40006MC 8ghaC 8ghmC 8ghnC 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
#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: 191915.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47171 #3: 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 |
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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 | Name: the Hir complex core / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: 495250 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
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