6OIT

CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1038/s41467-019-11759-9
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    Howard Hughes Medical Institute (HHMI), UCLA, Los Angeles, CA, 90095, USA. jacobsen@ucla.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein RDM1A, B175Arabidopsis thalianaMutation(s): 0 
Gene Names: RDM1At3g22680MWI23.5
UniProt
Find proteins for Q9LUJ3 (Arabidopsis thaliana)
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Go to UniProtKB:  Q9LUJ3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein DEFECTIVE IN MERISTEM SILENCING 3C, D, E, F449Arabidopsis thalianaMutation(s): 0 
Gene Names: DMS3IDN1At3g49250F2K15.110
UniProt
Find proteins for Q94A79 (Arabidopsis thaliana)
Explore Q94A79 
Go to UniProtKB:  Q94A79
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein CHROMATIN REMODELING 35G71Arabidopsis thalianaMutation(s): 0 
Gene Names: DRD1CHR35DMS1At2g16390F16F14.11
UniProt
Find proteins for Q9SIW2 (Arabidopsis thaliana)
Explore Q9SIW2 
Go to UniProtKB:  Q9SIW2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM130272
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesR01GM071940

Revision History  (Full details and data files)

  • 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