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Yorodumi- PDB-5iay: NMR structure of UHRF1 Tandem Tudor Domains in a complex with Spa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iay | |||||||||
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Title | NMR structure of UHRF1 Tandem Tudor Domains in a complex with Spacer peptide | |||||||||
Components |
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Keywords | LIGASE / UHRF1 / TTD / Spacer | |||||||||
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 / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / 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 | |||||||||
Authors | Fang, J. / Cheng, J. / Wang, J. / Zhang, Q. / Liu, M. / Gong, R. / Wang, P. / Zhang, X. / Feng, Y. / Lan, W. ...Fang, J. / Cheng, J. / Wang, J. / Zhang, Q. / Liu, M. / Gong, R. / Wang, P. / Zhang, X. / Feng, Y. / Lan, W. / Gong, Z. / Tang, C. / Wong, J. / Yang, H. / Cao, C. / Xu, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2016 Title: Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition Authors: Fang, J. / Cheng, J. / Wang, J. / Zhang, Q. / Liu, M. / Gong, R. / Wang, P. / Zhang, X. / Feng, Y. / Lan, W. / Gong, Z. / Tang, C. / Wong, J. / Yang, H. / Cao, C. / Xu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iay.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5iay.ent.gz | 872.8 KB | Display | PDB format |
PDBx/mmJSON format | 5iay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iay_validation.pdf.gz | 420.7 KB | Display | wwPDB validaton report |
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Full document | 5iay_full_validation.pdf.gz | 700.5 KB | Display | |
Data in XML | 5iay_validation.xml.gz | 77.1 KB | Display | |
Data in CIF | 5iay_validation.cif.gz | 98.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/5iay ftp://data.pdbj.org/pub/pdb/validation_reports/ia/5iay | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 17804.875 Da / Num. of mol.: 1 / Fragment: UNP residues 134-285 Source method: isolated from a genetically manipulated source Details: UHRF1 Tandem Tudor Domains / 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: 1606.849 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: UHRF1(642-658) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T88*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Details: PBS Buffer:pH 7.4, 10% D2O, 0.01% NaN3 / Ionic strength units: Not defined / Label: NMR condition / pH: 7.4 / Temperature: 297.15 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: 3 | |||||||||||||||||||||
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 |