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Yorodumi- EMDB-1646: Structure of the Human Dicer-TRBP Complex by Electron Microscopy -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1646 | |||||||||
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Title | Structure of the Human Dicer-TRBP Complex by Electron Microscopy | |||||||||
Map data | This is the 3D volume of human Dicer-TRBP complex | |||||||||
Sample |
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Keywords | Dicer Enzyme / Ribonuclease III / MicroRNA Processing / Single Particle Electron Microscopy | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Lau PW / Potter CS / Carragher B / MacRae IJ | |||||||||
Citation | Journal: Structure / Year: 2009 Title: Structure of the human Dicer-TRBP complex by electron microscopy. Authors: Pick-Wei Lau / Clinton S Potter / Bridget Carragher / Ian J MacRae / Abstract: Dicer is a specialized ribonuclease that initiates RNA interference (RNAi) by cleaving double-stranded RNA (dsRNA) into small RNA fragments about 22 nucleotides long. Here, we present the three- ...Dicer is a specialized ribonuclease that initiates RNA interference (RNAi) by cleaving double-stranded RNA (dsRNA) into small RNA fragments about 22 nucleotides long. Here, we present the three-dimensional structure of human Dicer bound to the protein TRBP at approximately 20 A resolution determined by negative-stain electron microscopy (EM) and single-particle analysis. Our analysis reveals that the Dicer-TRBP complex is an L-shaped molecule with a long edge of 150 A and a 100 A extension on one end. A surface trench runs the length of the long edge of the molecule, defining a putative dsRNA-binding site. Docking the crystal structure of Giardia Dicer, which represents the nuclease core of human Dicer, into the EM map suggests two possible overall molecular architectures for human Dicer. These results offer insights into the structure of Dicer proteins found in multicellular organisms and provide a conceptual framework for understanding the initiation of RNAi. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1646.map.gz | 4.5 MB | EMDB map data format | |
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Header (meta data) | emd-1646-v30.xml emd-1646.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | EMD-1646_image.png | 104 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1646 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1646 | HTTPS FTP |
-Validation report
Summary document | emd_1646_validation.pdf.gz | 186.4 KB | Display | EMDB validaton report |
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Full document | emd_1646_full_validation.pdf.gz | 185.5 KB | Display | |
Data in XML | emd_1646_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1646 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1646 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1646.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the 3D volume of human Dicer-TRBP complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.093 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Dicer-TRBP complex
Entire | Name: Dicer-TRBP complex |
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Components |
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-Supramolecule #1000: Dicer-TRBP complex
Supramolecule | Name: Dicer-TRBP complex / type: sample / ID: 1000 / Details: The sample was mostly monodisperse Oligomeric state: One human Dicer binds to one TRBP molecule Number unique components: 2 |
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Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Human Dicer
Macromolecule | Name: Human Dicer / type: protein_or_peptide / ID: 1 / Name.synonym: hDicer / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 220 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: Baculovirus |
-Macromolecule #2: TAR RNA binding protein
Macromolecule | Name: TAR RNA binding protein / type: protein_or_peptide / ID: 2 / Name.synonym: TRBP / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 30 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: Baculovirus |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: 150mM KCl, 20mM HEPES |
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Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 2% w/v uranyl acetate for approximately 20 seconds. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | May 31, 2009 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 947 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus min: 0.15 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Single tilt room temperature grid holder / Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Whole image |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN, SPIDER / Number images used: 129554 |
Final two d classification | Number classes: 711 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | PDBEntryID_givenInChain. Protocol: Rigid Body. Manual docking |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |