+Open data
-Basic information
Entry | Database: PDB / ID: 6ved | ||||||
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Title | Solution structure of the TTD and linker region of UHRF1 | ||||||
Components | E3 ubiquitin-protein ligase UHRF1 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / Histone / Tandem Tudor Domain / UHRF1 / H3K9me3 | ||||||
Function / homology | Function and homology information H3K9me3 modified histone binding / histone H3 ubiquitin ligase activity / 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 ...H3K9me3 modified histone binding / histone H3 ubiquitin ligase activity / 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 / methylated histone binding / positive regulation of protein metabolic process / 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 / spindle / nuclear matrix / 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 / molecular dynamics | ||||||
Authors | Lemak, A. / Houliston, S. / Duan, S. / Ong, M.S. / Arrowsmith, C.H. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1. Authors: Tauber, M. / Kreuz, S. / Lemak, A. / Mandal, P. / Yerkesh, Z. / Veluchamy, A. / Al-Gashgari, B. / Aljahani, A. / Cortes-Medina, L.V. / Azhibek, D. / Fan, L. / Ong, M.S. / Duan, S. / ...Authors: Tauber, M. / Kreuz, S. / Lemak, A. / Mandal, P. / Yerkesh, Z. / Veluchamy, A. / Al-Gashgari, B. / Aljahani, A. / Cortes-Medina, L.V. / Azhibek, D. / Fan, L. / Ong, M.S. / Duan, S. / Houliston, S. / Arrowsmith, C.H. / Fischle, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ved.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ved.ent.gz | 870.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ved.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ved_validation.pdf.gz | 535.9 KB | Display | wwPDB validaton report |
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Full document | 6ved_full_validation.pdf.gz | 876 KB | Display | |
Data in XML | 6ved_validation.xml.gz | 98.4 KB | Display | |
Data in CIF | 6ved_validation.cif.gz | 113.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/6ved ftp://data.pdbj.org/pub/pdb/validation_reports/ve/6ved | HTTPS FTP |
-Related structure data
Related structure data | 6veeC 6vfoC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 19475.812 Da / Num. of mol.: 1 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, RING-type E3 ubiquitin transferase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 250 uM [U-99% 13C; U-99% 15N] TTD-linker, 150 mM sodium chloride, 25 mM sodium phosphate, 5 mM DTT, 2 mM beta-mercaptoethanol, 2 mM TCEP, 95% H2O/5% D2O Label: double labeled / Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 150 mM / Label: condition_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | |||||||||||||||
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 |