+Open data
-Basic information
Entry | Database: PDB / ID: 6v41 | |||||||||
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Title | crystal structure of CDY1 chromodomain bound to H3K9me3 | |||||||||
Components |
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Keywords | TRANSFERASE / structural genomics consortium / SGC | |||||||||
Function / homology | Function and homology information Chromatin modifying enzymes / epigenetic regulation of gene expression / histone acetyltransferase activity / histone acetyltransferase / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation ...Chromatin modifying enzymes / epigenetic regulation of gene expression / histone acetyltransferase activity / histone acetyltransferase / methylated histone binding / 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 / 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 / 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 / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.603 Å | |||||||||
Authors | Qin, S. / Tempel, W. / Walker, J.R. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: Cell Chem Biol / Year: 2020 Title: Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Authors: Dong, C. / Liu, Y. / Lyu, T.J. / Beldar, S. / Lamb, K.N. / Tempel, W. / Li, Y. / Li, Z. / James, L.I. / Qin, S. / Wang, Y. / Min, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v41.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v41.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6v41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v41 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v41 | HTTPS FTP |
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-Related structure data
Related structure data | 2mj8C 6v2dC 6v2hC 6v2rC 6v2sC 6v3nC 6v8wC 4haeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m36uhg / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7642.388 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDY1, CDY1A, CDY1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6F8, histone acetyltransferase | ||||
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#2: Protein/peptide | Mass: 1607.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431 | ||||
#3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4 M sodium citrate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 30, 2014 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.6→23.36 Å / Num. obs: 8814 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.03 / Net I/σ(I): 43.4 | ||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4hae Resolution: 1.603→23.301 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.971 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.097 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: 22.062 Å2
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Refinement step | Cycle: LAST / Resolution: 1.603→23.301 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 / % reflection obs: 100 %
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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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