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Yorodumi- PDB-7xi9: Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ub... -
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-Basic information
Entry | Database: PDB / ID: 7xi9 | |||||||||||||||
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Title | Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form) | |||||||||||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA methyltransferase / TRANSFERASE-DNA COMPLEX | |||||||||||||||
Function / homology | Function and homology information chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation ...chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / STAT3 nuclear events downstream of ALK signaling / female germ cell nucleus / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / Nuclear events stimulated by ALK signaling in cancer / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / DNA methylation / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / promoter-specific chromatin binding / cellular response to amino acid stimulus / NoRC negatively regulates rRNA expression / methylation / negative regulation of gene expression / DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å | |||||||||||||||
Authors | Onoda, H. / Kikuchi, A. / Kori, S. / Yoshimi, S. / Yamagata, A. / Arita, K. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for activation of DNMT1. Authors: Amika Kikuchi / Hiroki Onoda / Kosuke Yamaguchi / Satomi Kori / Shun Matsuzawa / Yoshie Chiba / Shota Tanimoto / Sae Yoshimi / Hiroki Sato / Atsushi Yamagata / Mikako Shirouzu / Naruhiko ...Authors: Amika Kikuchi / Hiroki Onoda / Kosuke Yamaguchi / Satomi Kori / Shun Matsuzawa / Yoshie Chiba / Shota Tanimoto / Sae Yoshimi / Hiroki Sato / Atsushi Yamagata / Mikako Shirouzu / Naruhiko Adachi / Jafar Sharif / Haruhiko Koseki / Atsuya Nishiyama / Makoto Nakanishi / Pierre-Antoine Defossez / Kyohei Arita / Abstract: DNMT1 is an essential enzyme that maintains genomic DNA methylation, and its function is regulated by mechanisms that are not yet fully understood. Here, we report the cryo-EM structure of human ...DNMT1 is an essential enzyme that maintains genomic DNA methylation, and its function is regulated by mechanisms that are not yet fully understood. Here, we report the cryo-EM structure of human DNMT1 bound to its two natural activators: hemimethylated DNA and ubiquitinated histone H3. We find that a hitherto unstudied linker, between the RFTS and CXXC domains, plays a key role for activation. It contains a conserved α-helix which engages a crucial "Toggle" pocket, displacing a previously described inhibitory linker, and allowing the DNA Recognition Helix to spring into the active conformation. This is accompanied by large-scale reorganization of the inhibitory RFTS and CXXC domains, allowing the enzyme to gain full activity. Our results therefore provide a mechanistic basis for the activation of DNMT1, with consequences for basic research and drug design. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xi9.cif.gz | 206.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xi9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7xi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xi9_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7xi9_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7xi9_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 7xi9_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/7xi9 ftp://data.pdbj.org/pub/pdb/validation_reports/xi/7xi9 | HTTPS FTP |
-Related structure data
Related structure data | 33200MC 7xibC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 143106.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT1 / Plasmid: pFastBac / Cell line (production host): sf-9 / Production host: Baculovirus expression vector pFastBac1-HM References: UniProt: P26358, DNA (cytosine-5-)-methyltransferase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3725.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3679.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 237 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-SAH / | #6: Water | ChemComp-HOH / | |
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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: 0.17 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||
Source (recombinant) | Organism: Baculovirus expression vector pFastBac1-HM / Cell: sf-9 | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: This sample was monodisperse by Size-exclusion chromatography | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot for 4 seconds before plunging |
-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 / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4068 |
Image scans | Width: 4092 / Height: 5760 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3798046 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138662 / Algorithm: EXACT BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Accession code: 6X9I / Initial refinement model-ID: 1 / PDB-ID: 6X9I / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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