+Open data
-Basic information
Entry | Database: PDB / ID: 5wle | |||||||||||||||
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Title | Crystal structure of the PPS PHD finger in complex with H3K4me3 | |||||||||||||||
Components |
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Keywords | HYDROLASE / Epigenetic / PHD / Histone / trimethylated | |||||||||||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides / small nuclear ribonucleoprotein complex / regulation of alternative mRNA splicing, via spliceosome / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation ...Hydrolases; Acting on acid anhydrides / small nuclear ribonucleoprotein complex / regulation of alternative mRNA splicing, via spliceosome / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / helicase activity / 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 / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / hydrolase activity / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus Similarity search - Function | |||||||||||||||
Biological species | Drosophila melanogaster (fruit fly) Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.952 Å | |||||||||||||||
Authors | Klein, B.J. / Kutateladze, T.G. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Structure / Year: 2017 Title: A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO. Authors: Tencer, A.H. / Gatchalian, J. / Klein, B.J. / Khan, A. / Zhang, Y. / Strahl, B.D. / van Wely, K.H.M. / Kutateladze, T.G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wle.cif.gz | 31 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wle.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/5wle ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wle | HTTPS FTP |
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-Related structure data
Related structure data | 5wlfC 4l7xS 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
#1: Protein | Mass: 7318.447 Da / Num. of mol.: 1 / Fragment: UNP residues 904-965 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pps, CG6525, Dmel_CG6525 / Production host: Escherichia coli (E. coli) References: UniProt: Q9VG78, Hydrolases; Acting on acid anhydrides | ||
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#2: Protein/peptide | Mass: 1350.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS | ||
#3: Chemical | #4: 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: 1.82 Å3/Da / Density % sol: 32.27 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 0.1 mM Tris and 24% PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.952→31.2 Å / Num. obs: 4556 / % possible obs: 98.72 % / Redundancy: 3.8 % / Net I/σ(I): 37.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L7X Resolution: 1.952→31.2 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.952→31.2 Å
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Refine LS restraints |
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LS refinement shell |
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