6OIS | pdb_00006ois

CryoEM structure of Arabidopsis DR complex (DMS3-RDM1)

• PDB DOI: https://doi.org/10.2210/pdb6OIS/pdb
• EM Map EMD-20080: EMDB EMDataResource

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


• Deposited: 2019-04-09 Released: 2019-07-24 
• Deposition Author(s): Wongpalee, S.P., Liu, S., Zhou, Z.H., Jacobsen, S.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation.

Wongpalee, S.P., Liu, S., Gallego-Bartolome, J., Leitner, A., Aebersold, R., Liu, W., Yen, L., Nohales, M.A., Kuo, P.H., Vashisht, A.A., Wohlschlegel, J.A., Feng, S., Kay, S.A., Zhou, Z.H., Jacobsen, S.E.

(2019) Nat Commun 10: 3916-3916

• PubMed: 31477705 
• DOI: https://doi.org/10.1038/s41467-019-11759-9
• Primary Citation Related Structures: 
  6OIS, 6OIT


• PubMed Abstract: 
  

  Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components of the DDR complex DRD1, DMS3 and RDM1, but the assembly process of this complex and the underlying mechanism for Pol V recruitment remain unknown. Here we show that all DDR complex components co-localize with Pol V, and we report the cryoEM structures of two complexes associated with Pol V recruitment-DR (DMS3-RDM1) and DDR' (DMS3-RDM1-DRD1 peptide), at 3.6 Å and 3.5 Å resolution, respectively. RDM1 dimerization at the center frames the assembly of the entire complex and mediates interactions between DMS3 and DRD1 with a stoichiometry of 1 DRD1:4 DMS3:2 RDM1. DRD1 binding to the DR complex induces a drastic movement of a DMS3 coiled-coil helix bundle. We hypothesize that both complexes are functional intermediates that mediate Pol V recruitment.

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Organizational Affiliation: 
• Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.
Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA.
California NanoSystems Institute (CNSI), UCLA, Los Angeles, CA, 90095, USA.
Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland.
Faculty of Science, University of Zürich, 8057, Zürich, Switzerland.
Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, 310058, Hangzhou, P. R. China.
Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA.
Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA. [e-mail].
California NanoSystems Institute (CNSI), UCLA, Los Angeles, CA, 90095, USA. [e-mail].
Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA. [e-mail].
Howard Hughes Medical Institute (HHMI), UCLA, Los Angeles, CA, 90095, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 239.43 kDa 
• Atom Count: 10,732 
• Modeled Residue Count: 1,365 
• Deposited Residue Count: 2,146 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein RDM1	A, B	175	Arabidopsis thaliana	Mutation(s): 0  Gene Names: RDM1, At3g22680, MWI23.5
UniProt
Find proteins for Q9LUJ3 (Arabidopsis thaliana) Explore Q9LUJ3  Go to UniProtKB:  Q9LUJ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein DEFECTIVE IN MERISTEM SILENCING 3	C, D, E, F	449	Arabidopsis thaliana	Mutation(s): 0  Gene Names: DMS3, IDN1, At3g49250, F2K15.110
UniProt
Find proteins for Q94A79 (Arabidopsis thaliana) Explore Q94A79  Go to UniProtKB:  Q94A79

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Wongpalee, S.P., Liu, S., Zhou, Z.H., Jacobsen, S.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM130272
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	R01GM071940

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2019-12-18
  Changes: Other
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references