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Yorodumi- PDB-6iis: Complex structure of the HRP3 PWWP domain with both a 16-bp TA-ri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iis | ||||||
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Title | Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me3-containing histone peptide | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / growth factor / PWWP domain / Hepatoma-derived growth factor-related protein 3 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information negative regulation of microtubule depolymerization / microtubule polymerization / Chromatin modifying enzymes / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / tubulin binding / Assembly of the ORC complex at the origin of replication / DNA methylation ...negative regulation of microtubule depolymerization / microtubule polymerization / Chromatin modifying enzymes / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / tubulin binding / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / growth factor activity / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / neuron projection development / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.358 Å | ||||||
Authors | Wang, Z. / Tian, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me3-containing histone peptide Authors: Wang, Z. / Tian, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iis.cif.gz | 122 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iis.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 6iis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6iis ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6iis | HTTPS FTP |
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-Related structure data
Related structure data | 6iipS 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
#1: Protein | Mass: 11578.261 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL3, HDGF2, HDGFRP3, CGI-142 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y3E1 #2: DNA chain | Mass: 4894.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Protein/peptide | Mass: 924.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS #4: 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: 1.85 Å3/Da / Density % sol: 33.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M NaCl, 0.1 M HEPES, pH 7.5, and 25% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 9478 / % possible obs: 91.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.35→2.39 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2 / Num. unique obs: 481 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IIP Resolution: 2.358→33.129 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 34.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.358→33.129 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: 51.0367 Å / Origin y: -17.8991 Å / Origin z: 230.9349 Å
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Refinement TLS group | Selection details: all |