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Yorodumi- PDB-6kdb: Crystal structure of human DNMT3B-DNMT3L in complex with DNA cont... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kdb | ||||||
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Title | Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpT site | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNMT3B / DNA methyltransferase / complex / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / negative regulation of DNA methylation-dependent heterochromatin formation ...retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / negative regulation of DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / DNA metabolic process / negative regulation of gene expression, epigenetic / male meiosis I / catalytic complex / heterochromatin / enzyme activator activity / DNA methylation / PRC2 methylates histones and DNA / condensed nuclear chromosome / Defective pyroptosis / stem cell differentiation / NoRC negatively regulates rRNA expression / placenta development / transcription corepressor activity / methylation / spermatogenesis / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.862 Å | ||||||
Authors | Lin, C.-C. / Chen, Y.-P. / Yang, W.-Z. / Shen, C.-K. / Yuan, H.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B. Authors: Lin, C.C. / Chen, Y.P. / Yang, W.Z. / Shen, J.C.K. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kdb.cif.gz | 471.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kdb.ent.gz | 381.5 KB | Display | PDB format |
PDBx/mmJSON format | 6kdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kdb_validation.pdf.gz | 1008.6 KB | Display | wwPDB validaton report |
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Full document | 6kdb_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6kdb_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 6kdb_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kdb ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kdb | HTTPS FTP |
-Related structure data
Related structure data | 6kdaC 6kdlC 6kdpC 6kdtC 5yx2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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