+
Open data
-
Basic information
Entry | Database: PDB / ID: 6lxe | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | DROSHA-DGCR8 complex | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | HYDROLASE/RNA BINDING PROTEIN / Ribonuclease / RNA BINDING PROTEIN / HYDROLASE-RNA BINDING PROTEIN complex | |||||||||||||||||||||
Function / homology | ![]() positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / primary miRNA binding / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / U4 snRNA 3'-end processing / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process ...positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / primary miRNA binding / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / U4 snRNA 3'-end processing / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process / primary miRNA processing / regulation of stem cell proliferation / ribonuclease III activity / microprocessor complex / pre-miRNA processing / MicroRNA (miRNA) biogenesis / termination of RNA polymerase II transcription / SMAD binding / R-SMAD binding / lipopolysaccharide binding / rRNA processing / double-stranded RNA binding / protein-macromolecule adaptor activity / site of double-strand break / regulation of inflammatory response / defense response to Gram-negative bacterium / postsynaptic density / nuclear body / defense response to Gram-positive bacterium / glutamatergic synapse / DNA damage response / heme binding / positive regulation of gene expression / nucleolus / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||||||||
![]() | Jin, W. / Wang, J. / Liu, C.P. / Wang, H.W. / Xu, R.M. | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() Title: Structural Basis for pri-miRNA Recognition by Drosha. Authors: Wenxing Jin / Jia Wang / Chao-Pei Liu / Hong-Wei Wang / Rui-Ming Xu / ![]() Abstract: A commencing and critical step in miRNA biogenesis involves processing of pri-miRNAs in the nucleus by Microprocessor. An important, but not completely understood, question is how Drosha, the ...A commencing and critical step in miRNA biogenesis involves processing of pri-miRNAs in the nucleus by Microprocessor. An important, but not completely understood, question is how Drosha, the catalytic subunit of Microprocessor, binds pri-miRNAs and correctly specifies cleavage sites. Here we report the cryoelectron microscopy structures of the Drosha-DGCR8 complex with and without a pri-miRNA. The RNA-bound structure provides direct visualization of the tertiary structure of pri-miRNA and shows that a helix hairpin in the extended PAZ domain and the mobile basic (MB) helix in the RNase IIIa domain of Drosha coordinate to recognize the single-stranded to double-stranded junction of RNA, whereas the dsRNA binding domain makes extensive contacts with the RNA stem. Furthermore, the RNA-free structure reveals an autoinhibitory conformation of the PAZ helix hairpin. These findings provide mechanistic insights into pri-miRNA cleavage site selection and conformational dynamics governing pri-miRNA recognition by the catalytic component of Microprocessor. | |||||||||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 233.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 156.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 709.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 726.3 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30006MC ![]() 6lxdC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 115390.578 Da / Num. of mol.: 1 / Mutation: E1045Q, E1222Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 86171.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Ternary complex of DROSHA-DGCR8 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109333 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 5B16 Accession code: 5B16 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
|