+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-20080 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of Arabidopsis DR complex (DMS3-RDM1) | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | SMC-hinge / Coiled-coil / SNF2 / RNA-directed DNA methylation / PLANT PROTEIN | |||||||||
Function / homology | ![]() RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / siRNA processing / regulatory ncRNA-mediated gene silencing / protein homodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Wongpalee SP / Liu S | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 59.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 11.9 KB 11.9 KB | Display Display | ![]() |
Images | ![]() | 67.2 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oisMC ![]() 6oitC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : DR complex of DMS3 with RDM1
Entire | Name: DR complex of DMS3 with RDM1 |
---|---|
Components |
|
-Supramolecule #1: DR complex of DMS3 with RDM1
Supramolecule | Name: DR complex of DMS3 with RDM1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Protein RDM1
Macromolecule | Name: Protein RDM1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.072426 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH SQDPSSMTME LRPSGDSGSS DVDAEISDGF SPLDTSHRDV ADEGSLLRRA EMYQDYMKQV PIPTNRGSLI PFTSWVGLS ISMKQLYGQP LHYLTNVLLQ RWDQSRFGTD SEEQRLDSII HPTKAEATIW LVEEIHRLTP SHLHMALLWR S DPMYHSFI DPIFPEK UniProtKB: Protein RDM1 |
-Macromolecule #2: Protein DEFECTIVE IN MERISTEM SILENCING 3
Macromolecule | Name: Protein DEFECTIVE IN MERISTEM SILENCING 3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 49.821352 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADLYPTGQQ ISFQTTPLNV QDPTRMMNLD QSSPVARNET QNGGGIAHAE FAMFNSKRLE SDLEAMGNKI KQHEDNLKFL KSQKNKMDE AIVDLQVHMS KLNSSPTPRS ENSDNSLQGE DINAQILRHE NSAAGVLSLV ETLHGAQASQ LMLTKGVVGV V AKLGKVND ...String: MADLYPTGQQ ISFQTTPLNV QDPTRMMNLD QSSPVARNET QNGGGIAHAE FAMFNSKRLE SDLEAMGNKI KQHEDNLKFL KSQKNKMDE AIVDLQVHMS KLNSSPTPRS ENSDNSLQGE DINAQILRHE NSAAGVLSLV ETLHGAQASQ LMLTKGVVGV V AKLGKVND ENLSQILSNY LGTRSMLAVV CRNYESVTAL EAYDNHGNID INAGLHCLGS SIGREIGDSF DAICLENLRP YV GQHIADD LQRRLDLLKP KLPNGECPPG FLGFAVNMIQ IDPAYLLCVT SYGYGLRETL FYNLFSRLQV YKTRADMISA LPC ISDGAV SLDGGIIRKT GIFNLGNRDE VNVRFAKPTA SRTMDNYSEA EKKMKELKWK KEKTLEDIKR EQVLREHAVF NFGK KKEEF VRCLAQSSCT NQPMNTPRGT LESGKETAAA KFERQHMDSS TSAA UniProtKB: Protein DEFECTIVE IN MERISTEM SILENCING 3 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 314414 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1) |