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Yorodumi- PDB-6pa7: The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pa7 | ||||||
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Title | The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. | ||||||
Components |
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Keywords | TRANSFERASE/DNA / methyltransferase / complex / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / DNA-methyltransferase activity / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / DNA-methyltransferase activity / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / XY body / cellular response to ethanol / response to vitamin A / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / catalytic complex / chromosome, centromeric region / heterochromatin / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / cellular response to amino acid stimulus / response to lead ion / NoRC negatively regulates rRNA expression / euchromatin / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / response to estradiol / cellular response to hypoxia / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / methylation / response to xenobiotic stimulus / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | ||||||
Authors | Xu, T.H. / Liu, M. / Zhou, X.E. / Liang, G. / Zhao, G. / Xu, H.E. / Melcher, K. / Jones, P.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2020 Title: Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Authors: Ting-Hai Xu / Minmin Liu / X Edward Zhou / Gangning Liang / Gongpu Zhao / H Eric Xu / Karsten Melcher / Peter A Jones / Abstract: CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially ...CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core, and they favour the methylation of linker DNA at positioned nucleosomes. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pa7.cif.gz | 520.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pa7.ent.gz | 383.1 KB | Display | PDB format |
PDBx/mmJSON format | 6pa7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pa7_validation.pdf.gz | 918 KB | Display | wwPDB validaton report |
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Full document | 6pa7_full_validation.pdf.gz | 931.1 KB | Display | |
Data in XML | 6pa7_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 6pa7_validation.cif.gz | 85.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/6pa7 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/6pa7 | HTTPS FTP |
-Related structure data
Related structure data | 20281MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897 #4: Protein | Mass: 13655.948 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 51327.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 51785.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules KPNS
#7: Protein | Mass: 77914.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase #8: Protein | Mass: 86294.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase |
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-Non-polymers , 2 types, 5 molecules
#9: Chemical | #10: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.52 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 65 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2190114 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 599344 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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