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- PDB-4jjn: Crystal structure of heterochromatin protein Sir3 in complex with... -
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Basic information
Entry | Database: PDB / ID: 4jjn | ||||||
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Title | Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome | ||||||
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![]() | DNA BINDING PROTEIN/DNA / BAH domain / silencing / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() sexual sporulation resulting in formation of a cellular spore / 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 ...sexual sporulation resulting in formation of a cellular spore / 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 / nuclear origin of replication recognition complex / 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 / mitotic DNA replication checkpoint signaling / 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 / DNA replication origin binding / Estrogen-dependent gene expression / rRNA transcription / subtelomeric heterochromatin formation / DNA replication initiation / Ub-specific processing proteases / heterochromatin / CENP-A containing nucleosome / heterochromatin formation / heterochromatin organization / nucleosome binding / nucleosomal DNA binding / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / single-stranded DNA binding / double-stranded DNA binding / nucleic acid binding / chromosome, telomeric region / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / nucleolus / mitochondrion / DNA binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, F. / Li, G. / Mohammed, A. / Lu, C. / Currie, M. / Johnson, A. / Moazed, D. | ||||||
![]() | ![]() Title: Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA. Authors: Wang, F. / Li, G. / Altaf, M. / Lu, C. / Currie, M.A. / Johnson, A. / Moazed, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 776.1 KB | Display | ![]() |
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PDB format | ![]() | 628.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.8 KB | Display | ![]() |
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Full document | ![]() | 533.1 KB | Display | |
Data in XML | ![]() | 46.3 KB | Display | |
Data in CIF | ![]() | 64.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
-Protein , 5 types, 10 molecules AEBFCGDHKL
#1: Protein | Mass: 15259.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c Gene: HHT1, HHT2, Histone H3, N2749, SIN2, YBR010W, YBR0201, YNL031C Production host: ![]() ![]() #2: Protein | Mass: 11264.194 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c Gene: HHF1, HHF2, Histone H4, N2752, YBR009C, YBR0122, YNL030W Production host: ![]() ![]() #3: Protein | Mass: 13881.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: H2A2, Histone H2A.2, HTA2, YBL003C, YBL0103 / Production host: ![]() ![]() #4: Protein | Mass: 14133.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: H2B2, Histone H2B.2, HTB2, YBL002W, YBL0104 / Production host: ![]() ![]() #5: Protein | Mass: 43655.582 Da / Num. of mol.: 2 / Mutation: D205N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CMT1, L9753.10, MAR2, SIR3, STE8, YLR442C / Plasmid: pET-Sumo / Production host: ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#6: DNA chain | Mass: 45138.770 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#7: DNA chain | Mass: 45610.043 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05 M sodium cacodylate, 32% 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.09→139.09 Å / Num. all: 61627 / Num. obs: 60025 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 78.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09→85.45 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.8658 Å / Origin y: -20.1545 Å / Origin z: 24.5817 Å
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Refinement TLS group | Selection details: ALL |