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Yorodumi- EMDB-6899: Full length cryo-EM structure of Drosophila-sumo-C3PO (sumo-TRAX ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6899 | |||||||||
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Title | Full length cryo-EM structure of Drosophila-sumo-C3PO (sumo-TRAX + translin) complex | |||||||||
Map data | Drosophila full length cryoEM structure of sumo-C3PO complex (sumo-TRAX translin) | |||||||||
Sample |
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Biological species | Drosophila (fruit flies) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.8 Å | |||||||||
Authors | Mo X / Yuan AY | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2018 Title: Structural insights into Drosophila-C3PO complex assembly and 'Dynamic Side Port' model in substrate entry and release. Authors: Xiaobing Mo / Xia Yang / Yuren Adam Yuan / Abstract: In Drosophila and human, component 3 promoter of RISC (C3PO), a heteromeric complex, enhances RISC assembly and promotes RISC activity. Here, we report crystal structure of full-length Drosophila ...In Drosophila and human, component 3 promoter of RISC (C3PO), a heteromeric complex, enhances RISC assembly and promotes RISC activity. Here, we report crystal structure of full-length Drosophila C3PO (E126Q), an inactive C3PO mutant displaying much weaker RNA binding ability, at 2.1 Å resolution. In addition, we also report the cryo-EM structures of full-length Drosophila C3PO (E126Q), C3PO (WT) and SUMO-C3PO (WT, sumo-TRAX + Translin) particles trapped at different conformations at 12, 19.7 and 12.8 Å resolutions, respectively. Crystal structure of C3PO (E126Q) displays a half-barrel architecture consisting of two Trax/Translin heterodimers, whereas cryo-EM structures of C3PO (E126Q), C3PO (WT) and SUMO-C3PO (WT) adopt a closed football-like shape with a hollow interior cavity. Remarkably, both cryo-EM structures of Drosophila C3PO (E126Q) and Drosophila SUMO-C3PO (WT) particles contain a wide side port (∼25 Å × ∼30 Å versus ∼15 Å × ∼20 Å) for RNA substrate entry and release, formed by a pair of anti-parallel packed long α1 helices of TRAX subunits. Notably, cryo-EM structure of SUMO-C3PO showed that four copies of extra densities belonging to N-terminal SUMO tag are located at the outside shell of SUMO-C3PO particle, which demonstrated that the stoichiometry of TRAX/Translin for the in vitro expressed and assembled full-length Drosophila-SUMO-C3PO particle is 4:4, suggesting Drosophila C3PO is composed by TRAX/translin at a ratio of 4:4. Remarkably, the comparison of the cryo-EM structures suggests that the C3PO side ports regulated by α1 helices of TRAX molecules are highly dynamic. Hence, we propose that C3PO particles could adopt a 'Dynamic Side Port' model to capture/digest nucleic acid duplex substrate and release the digested fragments through the dynamic side ports. | |||||||||
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_6899.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-6899-v30.xml emd-6899.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6899_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_6899.png | 101.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6899 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6899 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6899.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Drosophila full length cryoEM structure of sumo-C3PO complex (sumo-TRAX translin) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.69 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 : C3PO
Entire | Name: C3PO |
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Components |
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-Supramolecule #1: C3PO
Supramolecule | Name: C3PO / type: complex / ID: 1 / Parent: 0 Details: In Drosophila, component 3 promoter of RISC (C3PO)is a complex, consisting of 4 Trax/Translin heterodimers. |
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Source (natural) | Organism: Drosophila (fruit flies) |
Recombinant expression | Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) Recombinant strain: DH5a / Recombinant plasmid: pET-Duet |
Recombinant expression | Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) Recombinant strain: BL21 (DE3) / Recombinant plasmid: pET-Duet |
Molecular weight | Experimental: 320 KDa |
-Supramolecule #2: sumo-TRAX
Supramolecule | Name: sumo-TRAX / type: complex / ID: 2 / Parent: 1 / Details: Translin-associated factor X |
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-Supramolecule #3: Translin
Supramolecule | Name: Translin / type: complex / ID: 3 / Parent: 1 / Details: A key component in C3PO complex |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
Details: 20mM Tris (pH 7.4), 500mM NaCl, 1mM DTT and 2mM EDTA | |||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before pluning. | |||||||||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated defocus max: 5.0 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 47000 / Illumination mode: OTHER / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 70.0 K |
Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 20 / Number real images: 800 / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2 |
-Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 200 |
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