7DE9 | pdb_00007de9

crystal structure of Arabidopsis RDM15 tudor domain in complex with an H3K4me1 peptide

• PDB DOI: https://doi.org/10.2210/pdb7DE9/pdb

• Classification: GENE REGULATION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-03 Released: 2021-04-07 
• Deposition Author(s): Song, Z., Du, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.202 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation.

Niu, Q., Song, Z., Tang, K., Chen, L., Wang, L., Ban, T., Guo, Z., Kim, C., Zhang, H., Duan, C.G., Zhang, H., Zhu, J.K., Du, J., Lang, Z.

(2021) Nat Commun 12: 3367-3367

• PubMed: 34099688 
• DOI: https://doi.org/10.1038/s41467-021-23637-4
• Primary Citation Related Structures: 
  7DE9


• PubMed Abstract: 
  

  In plants, RNA-directed DNA methylation (RdDM) is a well-known de novo DNA methylation pathway that involves two plant-specific RNA polymerases, Pol IV and Pol V. In this study, we discovered and characterized an RdDM factor, RDM15. Through DNA methylome and genome-wide siRNA analyses, we show that RDM15 is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. We show that RDM15 contributes to Pol V-dependent downstream siRNA accumulation and interacts with NRPE3B, a subunit specific to Pol V. We also show that the C-terminal tudor domain of RDM15 specifically recognizes the histone 3 lysine 4 monomethylation (H3K4me1) mark. Structure analysis of RDM15 in complex with the H3K4me1 peptide showed that the RDM15 tudor domain specifically recognizes the monomethyllysine through an aromatic cage and a specific hydrogen bonding network; this chemical feature-based recognition mechanism differs from all previously reported monomethyllysine recognition mechanisms. RDM15 and H3K4me1 have similar genome-wide distribution patterns at RDM15-dependent RdDM target loci, establishing a link between H3K4me1 and RDM15-mediated RdDM in vivo. In summary, we have identified and characterized a histone H3K4me1-specific binding protein as an RdDM component, and structural analysis of RDM15 revealed a chemical feature-based lower methyllysine recognition mechanism.

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Organizational Affiliation: 
• Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry Universtiy, Fuzhou, China.
Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Science, Southern University of Science and Technology, Shenzhen, Guangdong, China. [e-mail].
Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 9.17 kDa 
• Atom Count: 542 
• Modeled Residue Count: 63 
• Deposited Residue Count: 81 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A	66	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At4g31880, F11C18.80, F11C18_80
UniProt
Find proteins for Q8GUP3 (Arabidopsis thaliana) Explore Q8GUP3  Go to UniProtKB:  Q8GUP3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	B [auth P]	15	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P59226 (Arabidopsis thaliana) Explore P59226  Go to UniProtKB:  P59226

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
MLZ	B [auth P]	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.202 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.579	α = 90
b = 36.963	β = 90
c = 46.678	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Song, Z., Du, J.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2021-06-23
  Changes: Database references
• Version 1.2: 2025-04-09
  Changes: Data collection, Database references, Structure summary