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Yorodumi- PDB-8alq: The Solution Structure of the Triple Mutant Methyl-CpG-Binding Do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8alq | ||||||
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Title | The Solution Structure of the Triple Mutant Methyl-CpG-Binding Domain from MeCP2 that Binds to Asymmetrically Modified DNA | ||||||
Components | Methyl-CpG-binding protein 2 | ||||||
Keywords | DNA BINDING PROTEIN / hmC-mC complex / gene regulation / methyl-CpG-binding domain (MBD) of MeCP2 | ||||||
Function / homology | Function and homology information double-stranded methylated DNA binding / negative regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Singh, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Epigenetic CpG duplex marks probed by an evolved DNA reader via a well-tempered conformational plasticity. Authors: Singh, H. / Das, C.K. / Buchmuller, B.C. / Schafer, L.V. / Summerer, D. / Linser, R. #1: Journal: Biorxiv / Year: 2022 Title: Epigenetic CpG Duplex Marks Probed by an Evolved DNA Reader via a Well-Tempered Conformational Plasticity Authors: Singh, H. / Das, C.K. / Buchmuller, B.C. / Eppmann, S. / Schafer, L.V. / Summerer, D. / Linser, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8alq.cif.gz | 369.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8alq.ent.gz | 312.7 KB | Display | PDB format |
PDBx/mmJSON format | 8alq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8alq_validation.pdf.gz | 408.5 KB | Display | wwPDB validaton report |
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Full document | 8alq_full_validation.pdf.gz | 467.4 KB | Display | |
Data in XML | 8alq_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 8alq_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/8alq ftp://data.pdbj.org/pub/pdb/validation_reports/al/8alq | HTTPS FTP |
-Related structure data
Related structure data | 8ajrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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: 11905.288 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Mecp2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8C5LDB3 |
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-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 | Ionic strength: 100 mM / Label: conditions_1 / pH: 6 pH* / Pressure: 1 atm / Temperature: 305 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |