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Open data
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Basic information
Entry | Database: PDB / ID: 6wav | ||||||
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Title | Crystal structure of PHF1 in complex with H3K36me3 substitution | ||||||
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![]() | GENE REGULATION / PHF1 / Tudor / H3K36me3-H39V / complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() histone methyltransferase binding / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / Chromatin modifying enzymes / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication ...histone methyltransferase binding / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / Chromatin modifying enzymes / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / DNA methylation / transcription corepressor binding / 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 / 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 / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / site of double-strand break / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / centrosome / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dong, C. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J.R. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19. Authors: Dong, C. / Nakagawa, R. / Oyama, K. / Yamamoto, Y. / Zhang, W. / Dong, A. / Li, Y. / Yoshimura, Y. / Kamiya, H. / Nakayama, J.I. / Ueda, J. / Min, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6watC ![]() 6wauC ![]() 4hczS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6938.849 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1377.678 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % / Mosaicity: 0.33 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 8, 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: 1.7→40.07 Å / Num. obs: 29381 / % possible obs: 93.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.029 / Rrim(I) all: 0.056 / Net I/σ(I): 16.4 / Num. measured all: 107846 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HCZ Resolution: 1.7→32.802 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.342 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.124 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.886 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→32.802 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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