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- PDB-6oit: CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1) -

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Basic information

Entry
Database: PDB / ID: 6oit
TitleCryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1)
Components
  • Protein CHROMATIN REMODELING 35
  • Protein DEFECTIVE IN MERISTEM SILENCING 3
  • Protein RDM1
KeywordsPLANT PROTEIN / SMC-hinge / Coiled-coil / SNF2 / RNA-directed DNA methylation
Function / homology
Function and homology information


RNA polymerase IV transcription regulator complex / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / heterochromatin organization / siRNA processing / positive regulation of chromatin binding / regulatory ncRNA-mediated gene silencing / DNA methylation-dependent constitutive heterochromatin formation / cellular response to exogenous dsRNA / defense response to fungus ...RNA polymerase IV transcription regulator complex / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / heterochromatin organization / siRNA processing / positive regulation of chromatin binding / regulatory ncRNA-mediated gene silencing / DNA methylation-dependent constitutive heterochromatin formation / cellular response to exogenous dsRNA / defense response to fungus / pericentric heterochromatin / helicase activity / hydrolase activity / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
SNF2 domain-containing protein CLSY/DRD1 / RDM1 protein domain / Protein RDM1, plant / RDM1 superfamily / RNA-directed DNA methylation 1 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Four Helix Bundle (Hemerythrin (Met), subunit A) ...SNF2 domain-containing protein CLSY/DRD1 / RDM1 protein domain / Protein RDM1, plant / RDM1 superfamily / RNA-directed DNA methylation 1 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Protein DEFECTIVE IN MERISTEM SILENCING 3 / Protein RDM1 / Protein CHROMATIN REMODELING 35
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWongpalee, S.P. / Liu, S. / Zhou, Z.H. / Jacobsen, S.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM130272 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R01GM071940 United States
CitationJournal: Nat Commun / Year: 2019
Title: CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation.
Authors: Somsakul Pop Wongpalee / Shiheng Liu / Javier Gallego-Bartolomé / Alexander Leitner / Ruedi Aebersold / Wanlu Liu / Linda Yen / Maria A Nohales / Peggy Hsuanyu Kuo / Ajay A Vashisht / James ...Authors: Somsakul Pop Wongpalee / Shiheng Liu / Javier Gallego-Bartolomé / Alexander Leitner / Ruedi Aebersold / Wanlu Liu / Linda Yen / Maria A Nohales / Peggy Hsuanyu Kuo / Ajay A Vashisht / James A Wohlschlegel / Suhua Feng / Steve A Kay / Z Hong Zhou / Steven E Jacobsen /
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 ...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.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Protein RDM1
B: Protein RDM1
C: Protein DEFECTIVE IN MERISTEM SILENCING 3
D: Protein DEFECTIVE IN MERISTEM SILENCING 3
E: Protein DEFECTIVE IN MERISTEM SILENCING 3
F: Protein DEFECTIVE IN MERISTEM SILENCING 3
G: Protein CHROMATIN REMODELING 35


Theoretical massNumber of molelcules
Total (without water)247,3467
Polymers247,3467
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein RDM1 / Protein RNA-directed DNA methylation 1


Mass: 20072.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RDM1, At3g22680, MWI23.5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LUJ3
#2: Protein
Protein DEFECTIVE IN MERISTEM SILENCING 3 / Protein INVOLVED IN DE NOVO 1


Mass: 49821.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DMS3, IDN1, At3g49250, F2K15.110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q94A79
#3: Protein Protein CHROMATIN REMODELING 35 / Protein DEFECTIVE IN MERISTEM SILENCING 1 / Protein DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1


Mass: 7915.782 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DRD1, CHR35, DMS1, At2g16390, F16F14.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SIW2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DDR' complex of DRD1 peptide with DMS3 and RDM1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 47.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
11RELION2.1final Euler assignment
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 620248 / Symmetry type: POINT

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