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Yorodumi- PDB-1guw: STRUCTURE OF THE CHROMODOMAIN FROM MOUSE HP1beta IN COMPLEX WITH ... -
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-Basic information
Entry | Database: PDB / ID: 1guw | ||||||
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Title | STRUCTURE OF THE CHROMODOMAIN FROM MOUSE HP1beta IN COMPLEX WITH THE LYSINE 9-METHYL HISTONE H3 N-TERMINAL PEPTIDE, NMR, 25 STRUCTURES | ||||||
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Keywords | CHROMATIN-BINDING / LYSINE METHYLATION / HETEROCHROMATIN / HISTONE MODIFICATION | ||||||
Function / homology | Function and homology information chromatin organization => GO:0006325 / Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / chromocenter / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines ...chromatin organization => GO:0006325 / Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / chromocenter / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / histone methyltransferase binding / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / DNA replication-dependent chromatin assembly / male pronucleus / female pronucleus / nuclear chromosome / site of DNA damage / chromosome, centromeric region / Chromatin modifying enzymes / pericentric heterochromatin / 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 / 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 / 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 / nucleosome / 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) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / molecular adaptor activity / nuclear body / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Nielsen, P.R. / Nietlispach, D. / Mott, H.R. / Callaghan, J.M. / Bannister, A. / Kouzarides, T. / Murzin, A.G. / Murzina, N.V. / Laue, E.D. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Structure of the Hp1 Chromodomain Bound to Histone H3 Methylated at Lysine 9 Authors: Nielsen, P.R. / Nietlispach, D. / Mott, H.R. / Callaghan, J.M. / Bannister, A. / Kouzarides, T. / Murzin, A.G. / Murzina, N.V. / Laue, E.D. #1: Journal: Embo J. / Year: 1997 Title: Structure of the Chromatin Binding (Chromo) Domain from Mouse Modifier Protein 1 Authors: Ball, L.J. / Murzina, N.V. / Broadhurst, R.W. / Raine, A.R. / Archer, S.J. / Stott, F.J. / Murzin, A.G. / Singh, P.B. / Domaille, P.J. / Laue, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1guw.cif.gz | 703.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1guw.ent.gz | 613.8 KB | Display | PDB format |
PDBx/mmJSON format | 1guw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/1guw ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1guw | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8694.559 Da / Num. of mol.: 1 / Fragment: CHROMODOMAIN, RESIDUES 8 - 80 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23197, UniProt: P83917*PLUS |
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#2: Protein/peptide | Mass: 1831.108 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TAIL, RESIDUES 1-18 / Source method: obtained synthetically Details: BOTH CHEMICALLY SYTHESIZED PEPTIDE AND PEPTIDE OBTAINED FROM EXPRESSION IN BACTERIA WERE USED. Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P16106, UniProt: P68433*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE 2D AND 3D NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN. FOR PROTEIN ASSIGMENTS THE SAMPLE CONTAINED AN EXCESS OF 1.2 FOLD OF UNLABELLED ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE 2D AND 3D NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN. FOR PROTEIN ASSIGMENTS THE SAMPLE CONTAINED AN EXCESS OF 1.2 FOLD OF UNLABELLED PEPTIDE. THE PEPTIDE WAS ASSIGNED USING 13C, 15N REJECTED NOESY AND TOCSY EXPERIMENTS ON A SAMPLE OF EXCESS 13C, 15N LABELLED PROTEIN TO UNLABELLED PEPTIDE. THE METHYL GROUP RESONANCES OF LYSINE 4 AND 9 OF THE PEPTIDE WERE CONFIRMED WITH THE HELP OF A 13C METHYL-SELECTIVELY LABELLED SAMPLE MIXED WITH UNLABELLED PROTEIN. INTERMOLECULAR CONTACTS WERE OBTAINED FROM A 13C/15N X-FILTERED NOESY SPECTRUM AND A 3D J(CH,NH)- SEPARATED NOESY SPECTRUM |
-Sample preparation
Details | Contents: 150 mM NACL, 20 mM PHOSPHATE BUFFER, 10% D2O |
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Sample conditions | pH: 5.5 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY OF 75 CONVERGED STRUCTURES Conformers calculated total number: 100 / Conformers submitted total number: 25 |