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Yorodumi- PDB-4kud: Crystal structure of N-terminal acetylated Sir3 BAH domain D205N ... -
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-Basic information
Entry | Database: PDB / ID: 4kud | ||||||
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Title | Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/TRANSCRIPTION/DNA / PROTEPROTEIN-DNA COMPLEX / nucleosome / BAH domain / silencing / nucleus / STRUCTURAL PROTEIN-TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / establishment of protein-containing complex localization to telomere / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / nuclear-transcribed mRNA catabolic process, non-stop decay / 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 / cupric reductase (NADH) activity / establishment of protein-containing complex localization to telomere / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / nuclear-transcribed mRNA catabolic process, non-stop decay / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / telomere tethering at nuclear periphery / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / chromatin silencing complex / 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 / postreplication repair / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / DNA replication origin binding / Estrogen-dependent gene expression / rRNA transcription / CENP-A containing nucleosome / subtelomeric heterochromatin formation / intracellular copper ion homeostasis / nucleosome binding / Ub-specific processing proteases / heterochromatin / nucleosomal DNA binding / heterochromatin formation / aerobic respiration / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / double-stranded DNA binding / single-stranded DNA binding / chromosome, telomeric region / nucleic acid binding / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.203 Å | ||||||
Authors | Yang, D. / Fang, Q. / Wang, M. / Ren, R. / Wang, H. / He, M. / Sun, Y. / Yang, N. / Xu, R.M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: N alpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain. Authors: Yang, D. / Fang, Q. / Wang, M. / Ren, R. / Wang, H. / He, M. / Sun, Y. / Yang, N. / 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 | 4kud.cif.gz | 409.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kud.ent.gz | 317.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kud_validation.pdf.gz | 521.9 KB | Display | wwPDB validaton report |
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Full document | 4kud_full_validation.pdf.gz | 542.2 KB | Display | |
Data in XML | 4kud_validation.xml.gz | 48.9 KB | Display | |
Data in CIF | 4kud_validation.cif.gz | 69.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/4kud ftp://data.pdbj.org/pub/pdb/validation_reports/ku/4kud | HTTPS FTP |
-Related structure data
Related structure data | 4kuiC 4kulC 1id3S 2fvuS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 5 types, 10 molecules AEBFCGDHKL
#1: Protein | Mass: 15391.007 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61830 #2: Protein | Mass: 11395.390 Da / Num. of mol.: 2 / Mutation: S2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02309 #3: Protein | Mass: 13997.177 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: HTA2, H2A2, YBL003C, YBL0103 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04912 #4: Protein | Mass: 14280.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02293 #6: Protein | Mass: 26773.307 Da / Num. of mol.: 2 / Fragment: BAH domain, UNP residues 2-219 / Mutation: D205N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10 / Cell (production host): sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06701 |
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-DNA chain / Non-polymers , 2 types, 68 molecules IJ
#5: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically #7: Water | ChemComp-HOH / | |
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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: 3.33 Å3/Da / Density % sol: 63.02 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 16% PEG 400, 0.1M KCl, 0.01M CaCl2, 0.05M sodium citrate(pH4.8), VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 53876 / Num. obs: 54233 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 81.9 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5345 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ID3, 2FVU Resolution: 3.203→45.386 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8268 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.968 Å2 / ksol: 0.276 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 219.78 Å2 / Biso mean: 94.6105 Å2 / Biso min: 39.49 Å2
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Refinement step | Cycle: LAST / Resolution: 3.203→45.386 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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