+Open data
-Basic information
Entry | Database: PDB / ID: 7xay | ||||||
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Title | Crystal structure of Hat1-Hat2-Asf1-H3-H4 | ||||||
Components |
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Keywords | TRANSFERASE / Histone acetyltransferase / Histones / Enzymatic activity / Histone chaperone | ||||||
Function / homology | Function and homology information H3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Rpd3L complex / HDACs deacetylate histones / Rpd3L-Expanded complex / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex ...H3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Rpd3L complex / HDACs deacetylate histones / Rpd3L-Expanded complex / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / acetyltransferase activator activity / histone H4 acetyltransferase activity / DNA replication-dependent chromatin assembly / SUMOylation of chromatin organization proteins / nucleosome disassembly / : / replication fork protection complex / RMTs methylate histone arginines / silent mating-type cassette heterochromatin formation / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / subtelomeric heterochromatin formation / rRNA transcription / histone acetyltransferase complex / CENP-A containing nucleosome / histone acetyltransferase activity / histone acetyltransferase / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / chromosome, telomeric region / electron transfer activity / periplasmic space / chromatin remodeling / iron ion binding / protein heterodimerization activity / DNA repair / chromatin binding / heme binding / regulation of DNA-templated transcription / DNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Aspergillus fumigatus Af293 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Yue, Y. / Yang, W.S. / Xu, R.M. | ||||||
Funding support | China, 1items
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Citation | Journal: Genes Dev. / Year: 2022 Title: Topography of histone H3-H4 interaction with the Hat1-Hat2 acetyltransferase complex. Authors: Yue, Y. / Yang, W.S. / Zhang, L. / Liu, C.P. / Xu, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xay.cif.gz | 211.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xay.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/7xay ftp://data.pdbj.org/pub/pdb/validation_reports/xa/7xay | HTTPS FTP |
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-Related structure data
Related structure data | 4pswS S: Starting model for refinement |
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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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Unit cell |
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-Components
-Protein , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 48211.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: cybC, HAT1, YPL001W, LPA16W, YP8132.12 / Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) References: UniProt: P0ABE7, UniProt: Q12341, histone acetyltransferase |
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#2: Protein | Mass: 45105.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: HAT2, YEL056W / Production host: Escherichia coli (E. coli) / References: UniProt: P39984 |
#3: Protein | Mass: 17545.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: asf1, AFUA_3G11030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WXX5 |
#4: Protein | Mass: 15259.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / References: UniProt: P61830 |
#5: Protein | Mass: 10719.587 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309 |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-COA / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 70.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris propane, pH 6.5, 20% PEG-3350, and 200 mM sodium nitrate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→98.59 Å / Num. obs: 29577 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.48 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.3→3.5 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 4740 / CC1/2: 0.742 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PSW Resolution: 3.3→22.4 Å / SU ML: 0.3833 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8647 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→22.4 Å
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Refine LS restraints |
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LS refinement shell |
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