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Open data
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Basic information
Entry | Database: PDB / ID: 5zba | ||||||||||||||||||||||||
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Title | Crystal structure of Rtt109-Asf1-H3-H4-CoA complex | ||||||||||||||||||||||||
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![]() | TRANSFERASE/STRUCTURAL PROTEIN / Histone / acetylation / chaperone / DNA replication / nucleosome assembly / DNA damage / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex | ||||||||||||||||||||||||
Function / homology | ![]() histone H3K56 acetyltransferase activity / sexual sporulation resulting in formation of a cellular spore / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / 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 ...histone H3K56 acetyltransferase activity / sexual sporulation resulting in formation of a cellular spore / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / 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 / acetyltransferase activator activity / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / nucleosome disassembly / 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 / 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 / subtelomeric heterochromatin formation / CENP-A containing nucleosome / histone acetyltransferase / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / chromosome, telomeric region / protein heterodimerization activity / DNA damage response / regulation of DNA-templated transcription / DNA binding / nucleus / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Zhang, L. / Serra-Cardona, A. / Zhou, H. / Wang, M. / Yang, N. / Zhang, Z. / Xu, R.M. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109. Authors: Zhang, L. / Serra-Cardona, A. / Zhou, H. / Wang, M. / Yang, N. / Zhang, Z. / 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 | ![]() | 158.8 KB | Display | ![]() |
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PDB format | ![]() | 117.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 738.7 KB | Display | ![]() |
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Full document | ![]() | 744.7 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zb9SC ![]() 5zbbC ![]() 2hueS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 59684.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_5G09540 / Plasmid: pET28a-smt3 / Production host: ![]() ![]() |
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#2: Protein | Mass: 21097.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: asf1, AFUA_3G11030 / Plasmid: pET28a / Production host: ![]() ![]() |
#3: Protein | Mass: 15391.007 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Plasmid: pETDuet / Production host: ![]() ![]() |
#4: Protein | Mass: 11395.390 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Plasmid: pETDuet / Production host: ![]() ![]() |
-Non-polymers , 2 types, 38 molecules ![](data/chem/img/COA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/IOD.gif)
#5: Chemical | ChemComp-COA / |
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#6: Chemical | ChemComp-IOD / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100mM sodium citrate, pH 5.0, 22% PEG 1500, 400mM sodium iodide |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→50 Å / Num. obs: 16416 / % possible obs: 99.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 68.52 Å2 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.08 / Rrim(I) all: 0.196 / Χ2: 1.147 / Net I/σ(I): 4.3 / Num. measured all: 85255 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZB9, 2HUE Resolution: 3.5→42.825 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.75 / Stereochemistry target values: ML
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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 max: 129.19 Å2 / Biso mean: 65.8467 Å2 / Biso min: 42.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→42.825 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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