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Yorodumi- PDB-2b2u: Tandem chromodomains of human CHD1 complexed with Histone H3 Tail... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b2u | |||||||||
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Title | Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and dimethylarginine 2 | |||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / CHD / Chromodomain / three stranded antiparallel Beta sheet / alpha helix linker / histone H3 / asymmetric dimethylarginine / trimethyllysine | |||||||||
Function / homology | Function and homology information nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling ...nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / Chromatin modifying enzymes / epigenetic regulation of gene expression / 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 / helicase activity / 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 / 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 / DNA helicase / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Flanagan IV, J.F. / Mi, L.-Z. / Chruszcz, M. / Cymborowski, M. / Clines, K.L. / Kim, Y. / Minor, W. / Rastinejad, F. / Khorasanizadeh, S. | |||||||||
Citation | Journal: Nature / Year: 2005 Title: Double chromodomains cooperate to recognize the methylated histone H3 tail. Authors: Flanagan, J.F. / Mi, L.Z. / Chruszcz, M. / Cymborowski, M. / Clines, K.L. / Kim, Y. / Minor, W. / Rastinejad, F. / Khorasanizadeh, S. | |||||||||
History |
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Remark 300 | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ACCORDING TO ...THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ACCORDING TO AUTHORS, THE BIOLOGICAL UNIT IS UNKNOWN. | |||||||||
Remark 999 | SEQUENCE C-Terminal tyrosine at position 16 in chain D does not exist in Histone 3 naturally |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b2u.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b2u.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 2b2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/2b2u ftp://data.pdbj.org/pub/pdb/validation_reports/b2/2b2u | HTTPS FTP |
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-Related structure data
Related structure data | 2b2tSC 2b2vC 2b2wC 2b2yC 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: 22146.762 Da / Num. of mol.: 2 / Fragment: residues 268-443 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14646 #2: Protein | | Mass: 13694.292 Da / Num. of mol.: 1 / Fragment: residues 268-373 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14646 #3: Protein/peptide | | Mass: 1798.096 Da / Num. of mol.: 1 / Fragment: residues 1-15 / Source method: obtained synthetically Details: This sequence occurs naturally in Homo Sapiens (humans). References: UniProt: P68431 |
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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: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 283 K / pH: 8 Details: 4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 8, 2005 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→32.5 Å / Num. obs: 11356 / % possible obs: 94.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.11 / Rsym value: 0.378 / % possible all: 70.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B2T Resolution: 2.95→20 Å / Isotropic thermal model: ISOTROPIC / σ(F): 203 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Bsol: 10 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→20 Å
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Refine LS restraints |
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Xplor file |
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