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Yorodumi- PDB-7yhp: CryoEM structure of Arabidopsis ROS1 in complex with 5mC-dsDNA at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yhp | ||||||
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Title | CryoEM structure of Arabidopsis ROS1 in complex with 5mC-dsDNA at 3.1 Angstroms resolution | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / ROS1 / DNA glycosylase / DNA demethylation / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information DNA demethylase activity / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / : / DNA N-glycosylase activity / male sex determination / defense response to fungus / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity ...DNA demethylase activity / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / : / DNA N-glycosylase activity / male sex determination / defense response to fungus / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Deactivation of the beta-catenin transactivating complex / brain development / base-excision repair / neuron differentiation / 4 iron, 4 sulfur cluster binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Du, X. / Du, J. | ||||||
Funding support | 1items
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Citation | Journal: Nat Plants / Year: 2023 Title: Molecular basis of the plant ROS1-mediated active DNA demethylation. Authors: Xuan Du / Zhenlin Yang / Guohui Xie / Changshi Wang / Laixing Zhang / Kaige Yan / Maojun Yang / Sisi Li / Jian-Kang Zhu / Jiamu Du / Abstract: Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly ...Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly excise 5-methyl-cytosine (5mC), representing an efficient DNA demethylation pathway distinct from that of animals. Here, we report the cryo-electron microscopy structures of an Arabidopsis ROS1 catalytic fragment in complex with substrate DNA, mismatch DNA and reaction intermediate, respectively. The substrate 5mC is flipped-out from the DNA duplex and subsequently recognized by the ROS1 base-binding pocket through hydrophobic and hydrogen-bonding interactions towards the 5-methyl group and Watson-Crick edge respectively, while the different protonation states of the bases determine the substrate preference for 5mC over T:G mismatch. Together with the structure of the reaction intermediate complex, our structural and biochemical studies revealed the molecular basis for substrate specificity, as well as the reaction mechanism underlying 5mC demethylation by the ROS1/DME family of plant-specific DNA demethylases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yhp.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yhp.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 7yhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yhp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7yhp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7yhp_validation.xml.gz | 28 KB | Display | |
Data in CIF | 7yhp_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/7yhp ftp://data.pdbj.org/pub/pdb/validation_reports/yh/7yhp | HTTPS FTP |
-Related structure data
Related structure data | 33835MC 7yhoC 7yhqC 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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-Components
#1: Protein | Mass: 86260.859 Da / Num. of mol.: 1 / Mutation: D971N Source method: isolated from a genetically manipulated source Details: Fusion protein of residues 56 to 130 of database UNP Q05066, Linker, residues 511 to 1393 of database UNP Q9SJQ6, with deletion of residues 665-835 and 1074-1109. Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Arabidopsis thaliana (thale cress) Gene: SRY, TDF, ROS1, DML1, At2g36490, F1O11.12 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q05066, UniProt: Q9SJQ6, DNA-(apurinic or apyrimidinic site) lyase |
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#2: DNA chain | Mass: 12336.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) |
#3: DNA chain | Mass: 12292.913 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) |
#4: Chemical | ChemComp-SF4 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Average exposure time: 1.3467 sec. / Electron dose: 1.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116523 / Symmetry type: POINT | ||||||||||||||||||||||||
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