+Open data
-Basic information
Entry | Database: PDB / ID: 5zbb | ||||||||||||||||||||||||
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Title | Crystal structure of Rtt109-Asf1-H3-H4 complex | ||||||||||||||||||||||||
Components |
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Keywords | TRANSFERASE/STRUCTURAL PROTEIN / Histone / acetylation / chaperone / DNA replication / nucleosome assembly / DNA damage / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex | ||||||||||||||||||||||||
Function / homology | Function and homology information histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / acetyltransferase activator activity ...histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / acetyltransferase activator 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 / CENP-A containing nucleosome / 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 / protein heterodimerization activity / DNA damage response / regulation of DNA-templated transcription / DNA binding / nucleus / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | Neosartorya fumigata (mold) Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å | ||||||||||||||||||||||||
Authors | Zhang, L. / Serra-Cardona, A. / Zhou, H. / Wang, M. / Yang, N. / Zhang, Z. / Xu, R.M. | ||||||||||||||||||||||||
Funding support | China, United States, 7items
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Citation | Journal: Cell / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zbb.cif.gz | 159 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zbb.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 5zbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/5zbb ftp://data.pdbj.org/pub/pdb/validation_reports/zb/5zbb | HTTPS FTP |
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-Related structure data
Related structure data | 5zb9SC 5zbaC 2hueS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_5G09540 / Plasmid: pET28a-smt3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4WUS9 |
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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.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: asf1, AFUA_3G11030 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4WXX5 |
#3: Protein | Mass: 15391.007 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Plasmid: pETDuet / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61830 |
#4: Protein | Mass: 11395.390 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Plasmid: pETDuet / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02309 |
-Non-polymers , 3 types, 25 molecules
#5: Chemical | ChemComp-IOD / #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-GOL / | |
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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: 2.82 Å3/Da / Density % sol: 56.31 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.6→50 Å / Num. obs: 15314 / % possible obs: 99.9 % / Redundancy: 18.9 % / Biso Wilson estimate: 58.44 Å2 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.058 / Rrim(I) all: 0.256 / Χ2: 0.922 / Net I/σ(I): 3.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZB9, 2HUE Resolution: 3.6→42.921 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.1 Å2 / Biso mean: 56.639 Å2 / Biso min: 18.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.6→42.921 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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