7YHO

CryoEM structure of Arabidopsis ROS1 in complex with TG mismatch dsDNA at 3.3 Angstroms resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of the plant ROS1-mediated active DNA demethylation.

Du, X.Yang, Z.Xie, G.Wang, C.Zhang, L.Yan, K.Yang, M.Li, S.Zhu, J.K.Du, J.

(2023) Nat Plants 9: 271-279

  • DOI: https://doi.org/10.1038/s41477-022-01322-8
  • Primary Citation of Related Structures:  
    7YHO, 7YHP, 7YHQ

  • PubMed 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 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.


  • Organizational Affiliation

    Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sex-determining region Y protein,DNA glycosylase/AP lyase ROS1757Homo sapiensArabidopsis thalianaMutation(s): 1 
Gene Names: SRYTDFROS1DML1At2g36490F1O11.12
EC: 4.2.99.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q9SJQ6 (Arabidopsis thaliana)
Explore Q9SJQ6 
Go to UniProtKB:  Q9SJQ6
Find proteins for Q05066 (Homo sapiens)
Explore Q05066 
Go to UniProtKB:  Q05066
PHAROS:  Q05066
GTEx:  ENSG00000184895 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ05066Q9SJQ6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (40-MER)40Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (40-MER)40Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-11-30 
  • Deposition Author(s): Du, X., Du, J.

Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references