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Open data
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Basic information
Entry | Database: PDB / ID: 7xay | ||||||
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Title | Crystal structure of Hat1-Hat2-Asf1-H3-H4 | ||||||
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![]() | TRANSFERASE / Histone acetyltransferase / Histones / Enzymatic activity / Histone chaperone | ||||||
Function / homology | ![]() sexual sporulation resulting in formation of a cellular spore / H3 histone acetyltransferase complex / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Rpd3L complex / Rpd3L-Expanded complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...sexual sporulation resulting in formation of a cellular spore / H3 histone acetyltransferase complex / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Rpd3L complex / Rpd3L-Expanded 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 / acetyltransferase activator activity / HDACs deacetylate histones / histone H4 acetyltransferase activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / NuRD complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / ESC/E(Z) complex / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / 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 / histone acetyltransferase complex / subtelomeric heterochromatin formation / CENP-A containing nucleosome / histone acetyltransferase activity / nucleosome binding / histone acetyltransferase / positive regulation of transcription elongation by RNA polymerase II / electron transport chain / regulation of protein phosphorylation / protein modification process / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / chromosome, telomeric region / periplasmic space / electron transfer activity / chromatin remodeling / iron ion binding / protein heterodimerization activity / DNA repair / chromatin binding / heme binding / regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yue, Y. / Yang, W.S. / Xu, R.M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.4 KB | Display | ![]() |
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PDB format | ![]() | 159.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.5 KB | Display | ![]() |
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Full document | ![]() | 813.3 KB | Display | |
Data in XML | ![]() | 38.5 KB | Display | |
Data in CIF | ![]() | 52.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pswS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 17545.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 15259.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Protein | Mass: 10719.587 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/COA.gif)
#6: Chemical | ChemComp-COA / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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