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Yorodumi- PDB-6oit: CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1) -
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-Basic information
Entry | Database: PDB / ID: 6oit | |||||||||
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Title | CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1) | |||||||||
Components |
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Keywords | PLANT PROTEIN / SMC-hinge / Coiled-coil / SNF2 / RNA-directed DNA methylation | |||||||||
Function / homology | Function and homology information regulation of gene silencing by regulatory ncRNA / RNA polymerase IV transcription regulator complex / regulation of post-transcriptional gene silencing by regulatory ncRNA / : / : / : / : / positive regulation of post-transcriptional gene silencing by RNA / gene silencing by siRNA-directed DNA methylation / RNA polymerase V complex ...regulation of gene silencing by regulatory ncRNA / RNA polymerase IV transcription regulator complex / regulation of post-transcriptional gene silencing by regulatory ncRNA / : / : / : / : / positive regulation of post-transcriptional gene silencing by RNA / gene silencing by siRNA-directed DNA methylation / RNA polymerase V complex / ATP-dependent chromatin remodeler activity => GO:0140658 / regulation of miRNA-mediated gene silencing / : / : / siRNA processing / regulatory ncRNA-mediated gene silencing / positive regulation of chromatin binding / 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 | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Wongpalee, S.P. / Liu, S. / Zhou, Z.H. / Jacobsen, S.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6oit.cif.gz | 278.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oit.ent.gz | 222.1 KB | Display | PDB format |
PDBx/mmJSON format | 6oit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oit ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oit | HTTPS FTP |
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-Related structure data
Related structure data | 20081MC 6oisC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | 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 | | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DDR' complex of DRD1 peptide with DMS3 and RDM1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 47.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 620248 / Symmetry type: POINT |