+Open data
-Basic information
Entry | Database: PDB / ID: 5iql | |||||||||
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Title | Crystal structure of YEATS2 YEATS bound to H3K27cr peptide | |||||||||
Components |
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Keywords | PROTEIN BINDING / beta sandwich | |||||||||
Function / homology | Function and homology information modification-dependent protein binding / ATAC complex / NuA4 histone acetyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / regulation of embryonic development / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization ...modification-dependent protein binding / ATAC complex / NuA4 histone acetyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / regulation of embryonic development / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / TBP-class protein binding / histone reader activity / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / regulation of cell cycle / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | |||||||||
Authors | Li, H. / Zhao, D. / Guan, H. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Res. / Year: 2016 Title: YEATS2 is a selective histone crotonylation reader. Authors: Zhao, D. / Guan, H. / Zhao, S. / Mi, W. / Wen, H. / Li, Y. / Zhao, Y. / Allis, C.D. / Shi, X. / Li, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iql.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iql.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 5iql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/5iql ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iql | HTTPS FTP |
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-Related structure data
Related structure data | 4tmpS 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: 15818.110 Da / Num. of mol.: 1 / Fragment: YEATS domain (UNP RESIDUES 201-332) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS2, KIAA1197 / Plasmid: pSUMOH10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ULM3 |
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#2: Protein/peptide | Mass: 839.960 Da / Num. of mol.: 1 / Fragment: H3 peptide (UNP RESIDUES 25-32) / Source method: obtained synthetically / Details: Kcr: lysine crotonylation / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.17 % / Mosaicity: 0.238 ° / Mosaicity esd: 0.005 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 0.1M Bis-Tris propane, 4.0 M NH4Ac, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2015 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 10507 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 40.84 Å2 / Rmerge(I) obs: 0.082 / Net I/av σ(I): 52.5 / Net I/σ(I): 12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 4TMP Resolution: 2.1→35.221 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.03 Å2 / Biso mean: 55.1106 Å2 / Biso min: 24.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→35.221 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: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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