+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12994 | |||||||||
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Title | Structure of the U2 5' module of the A3'-SSA complex | |||||||||
Map data | The U2 5' module of the A3'-SSA complex (tight mask) | |||||||||
Sample |
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Function / homology | Function and homology information U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / SAGA complex / U2 snRNP ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / U2 snRNA binding / regulation of DNA repair / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA processing / nuclear matrix / positive regulation of neuron projection development / mRNA splicing, via spliceosome / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / unidentified adenovirus / Human (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Cretu C / Pena V | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Authors: Constantin Cretu / Patricia Gee / Xiang Liu / Anant Agrawal / Tuong-Vi Nguyen / Arun K Ghosh / Andrew Cook / Melissa Jurica / Nicholas A Larsen / Vladimir Pena / Abstract: Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing ...Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)-a complex chaperoning the selection of branch and 3' splice sites. Here we report crystal structures of the SF3B module of the U2 snRNP in complex with spliceostatin and sudemycin FR901464 analogs, and the cryo-electron microscopy structure of a cross-exon prespliceosome-like complex arrested with spliceostatin A. The structures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an E-to-A prespliceosome intermediate by covalent coupling to a nucleophilic zinc finger belonging to the SF3B subunit PHF5A. These findings support a mechanism of intron recognition by the U2 snRNP as a toehold-mediated strand invasion and advance an unanticipated drug targeting concept. | |||||||||
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_12994.map.gz | 337.8 MB | EMDB map data format | |
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Header (meta data) | emd-12994-v30.xml emd-12994.xml | 40.1 KB 40.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12994_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_12994.png | 39.5 KB | ||
Masks | emd_12994_msk_1.map | 421.9 MB | Mask map | |
Others | emd_12994_additional_1.map.gz emd_12994_additional_2.map.gz emd_12994_additional_3.map.gz emd_12994_half_map_1.map.gz emd_12994_half_map_2.map.gz | 3.5 MB 334.4 MB 335.5 MB 337.2 MB 338.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12994 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12994 | HTTPS FTP |
-Validation report
Summary document | emd_12994_validation.pdf.gz | 402.9 KB | Display | EMDB validaton report |
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Full document | emd_12994_full_validation.pdf.gz | 402 KB | Display | |
Data in XML | emd_12994_validation.xml.gz | 24 KB | Display | |
Data in CIF | emd_12994_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12994 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12994 | HTTPS FTP |
-Related structure data
Related structure data | 7onbMC 7b0iC 7b91C 7b92C 7b9cC 7omfC 7opiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12994.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The U2 5' module of the A3'-SSA complex (tight mask) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12994_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally scaled/sharpened density of the U2 5' module
File | emd_12994_additional_1.map | ||||||||||||
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Annotation | Locally scaled/sharpened density of the U2 5' module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: U2 5' module's unsharpened density map (tight mask)
File | emd_12994_additional_2.map | ||||||||||||
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Annotation | U2 5' module's unsharpened density map (tight mask) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: U2 5' module's unsharpened density map (loose mask)
File | emd_12994_additional_3.map | ||||||||||||
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Annotation | U2 5' module's unsharpened density map (loose mask) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_12994_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_12994_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The U2 5' module of the A3'-SSA complex
+Supramolecule #1: The U2 5' module of the A3'-SSA complex
+Supramolecule #2: The U2 5' module of the A3'-SSA complex
+Supramolecule #3: MINX
+Macromolecule #1: Splicing factor 3B subunit 3
+Macromolecule #2: Splicing factor 3B subunit 5
+Macromolecule #3: Splicing factor 3B subunit 1
+Macromolecule #4: PHD finger-like domain-containing protein 5A
+Macromolecule #5: UNK
+Macromolecule #8: Splicing factor 3B subunit 2
+Macromolecule #9: Splicing factor 3A subunit 2
+Macromolecule #10: Splicing factor 3A subunit 3
+Macromolecule #11: Splicing factor 3B subunit 4
+Macromolecule #6: MINX
+Macromolecule #7: RNU2
+Macromolecule #12: spliceostatin A (form II)
+Macromolecule #13: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.24 mg/mL | ||||||||||||
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Buffer | pH: 7.9 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: The A3'-SSA complex was frozen in vitreous ice by applying ~2.2 uL crosslinked sample to both sides of a glow-discharged UltrAufoil R1.2/1.3 gold grid. The excess sample was blotted away for ...Details: The A3'-SSA complex was frozen in vitreous ice by applying ~2.2 uL crosslinked sample to both sides of a glow-discharged UltrAufoil R1.2/1.3 gold grid. The excess sample was blotted away for 2s using a blot force of 7 and the grid was snap frozen in liquid ethane cooled by liquid nitrogen.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10494 / Average exposure time: 2.0 sec. / Average electron dose: 41.41 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 81000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |