+Open data
-Basic information
Entry | Database: PDB / ID: 2lgg | ||||||
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Title | Structure of PHD domain of UHRF1 in complex with H3 peptide | ||||||
Components |
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Keywords | LIGASE/DNA BINDING PROTEIN / DNA Binding Protein/gene Regulation / LIGASE-DNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / mitotic spindle assembly ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / mitotic spindle assembly / protein autoubiquitination / heterochromatin / cis-regulatory region sequence-specific DNA binding / Chromatin modifying enzymes / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / telomere organization / positive regulation of protein metabolic process / 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 / replication fork / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RING-type E3 ubiquitin transferase / 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 / nuclear matrix / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / ubiquitin protein ligase 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 / histone binding / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nucleic acid binding / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Wang, C. / Shen, J. / Yang, Z. / Chen, P. / Zhao, B. / Hu, W. / Lan, W. / Tong, X. / Wu, H. / Li, G. / Cao, C. | ||||||
Citation | Journal: Cell Res. / Year: 2011 Title: Structural basis for site-specific reading of unmodified R2 of histone H3 tail by UHRF1 PHD finger. Authors: Wang, C. / Shen, J. / Yang, Z. / Chen, P. / Zhao, B. / Hu, W. / Lan, W. / Tong, X. / Wu, H. / Li, G. / Cao, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lgg.cif.gz | 474.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lgg.ent.gz | 396.1 KB | Display | PDB format |
PDBx/mmJSON format | 2lgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/2lgg ftp://data.pdbj.org/pub/pdb/validation_reports/lg/2lgg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7849.898 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 298-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli) References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein/peptide | Mass: 1308.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P68431*PLUS |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1 mM / Component: entity_1-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.15 / pH: 7.4 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR constraints | NOE constraints total: 930 / NOE intraresidue total count: 309 / NOE long range total count: 136 / NOE medium range total count: 141 / NOE sequential total count: 328 | |||||||||
NMR representative | Selection criteria: closest to the average | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1 | |||||||||
NMR ensemble rms | Distance rms dev: 1.16 Å / Distance rms dev error: 0.31 Å |