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Yorodumi- PDB-2lgk: NMR Structure of UHRF1 PHD domains in a complex with histone H3 p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lgk | ||||||
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Title | NMR Structure of UHRF1 PHD domains in a complex with histone H3 peptide | ||||||
Components |
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Keywords | LIGASE/DNA BINDING PROTEIN / UHRF1 / PHD / Histone H3 / 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 / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / 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 / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / heterochromatin / positive regulation of protein metabolic process / methylated histone binding / epigenetic regulation of gene expression / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / euchromatin / heterochromatin formation / nuclear matrix / spindle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / protein ubiquitination / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, 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 | 2lgk.cif.gz | 477.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lgk.ent.gz | 400.3 KB | Display | PDB format |
PDBx/mmJSON format | 2lgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lgk_validation.pdf.gz | 626.6 KB | Display | wwPDB validaton report |
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Full document | 2lgk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2lgk_validation.xml.gz | 62.8 KB | Display | |
Data in CIF | 2lgk_validation.cif.gz | 82.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/2lgk ftp://data.pdbj.org/pub/pdb/validation_reports/lg/2lgk | HTTPS FTP |
-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) / 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: 1350.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.5 mM [U-100% 13C; U-100% 15N] entity_1-1, 1.8 mM entity_2-2, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 150 / pH: 7 / Pressure: ambient / Temperature: 293.13 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: 969 / NOE intraresidue total count: 357 / NOE long range total count: 137 / NOE medium range total count: 128 / NOE sequential total count: 329 / Hydrogen bond constraints total count: 5 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 40 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
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: 0.022 Å / Distance rms dev error: 0.00026 Å |