+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13793 | |||||||||
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Title | Human 17S U2 snRNP 5' domain core | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information U11/U12 snRNP / chromatin-protein adaptor activity / B-WICH complex / splicing factor binding / protein localization to site of double-strand break / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / poly-ADP-D-ribose modification-dependent protein binding / : / U2-type spliceosomal complex ...U11/U12 snRNP / chromatin-protein adaptor activity / B-WICH complex / splicing factor binding / protein localization to site of double-strand break / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / poly-ADP-D-ribose modification-dependent protein binding / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / SAGA complex / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / regulation of DNA repair / Cajal body / U2 snRNA binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / double-strand break repair via homologous recombination / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA splicing, via spliceosome / fibrillar center / mRNA processing / nuclear matrix / site of double-strand break / RNA helicase activity / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.21 Å | |||||||||
Authors | Tholen J / Galej WP | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Science / Year: 2022 Title: Structural basis of branch site recognition by the human spliceosome. Authors: Jonas Tholen / Michal Razew / Felix Weis / Wojciech P Galej / Abstract: Recognition of the intron branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is a critical event during spliceosome assembly. In mammals, BS sequences are poorly conserved, and ...Recognition of the intron branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is a critical event during spliceosome assembly. In mammals, BS sequences are poorly conserved, and unambiguous intron recognition cannot be achieved solely through a base-pairing mechanism. We isolated human 17 U2 snRNP and reconstituted in vitro its adenosine 5´-triphosphate (ATP)–dependent remodeling and binding to the pre–messenger RNA substrate. We determined a series of high-resolution (2.0 to 2.2 angstrom) structures providing snapshots of the BS selection process. The substrate-bound U2 snRNP shows that SF3B6 stabilizes the BS:U2 snRNA duplex, which could aid binding of introns with poor sequence complementarity. ATP-dependent remodeling uncoupled from substrate binding captures U2 snRNA in a conformation that competes with BS recognition, providing a selection mechanism based on branch helix stability. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13793.map.gz | 693.9 MB | EMDB map data format | |
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Header (meta data) | emd-13793-v30.xml emd-13793.xml | 33.9 KB 33.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13793_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_13793.png | 115.7 KB | ||
Masks | emd_13793_msk_1.map | 1000 MB | Mask map | |
Others | emd_13793_half_map_1.map.gz emd_13793_half_map_2.map.gz | 694.7 MB 694.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13793 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13793 | HTTPS FTP |
-Related structure data
Related structure data | 7q3lMC 7q4oC 7q4pC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13793.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.64 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13793_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13793_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13793_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 17S U2 snRNP
+Supramolecule #1: 17S U2 snRNP
+Supramolecule #2: 17S U2 snRNP
+Supramolecule #3: HIV Tat-specific factor 1
+Macromolecule #1: Splicing factor 3B subunit 2
+Macromolecule #2: Splicing factor 3B subunit 3
+Macromolecule #3: Splicing factor 3B subunit 5
+Macromolecule #4: PHD finger-like domain-containing protein 5A
+Macromolecule #6: Splicing factor 3A subunit 3
+Macromolecule #7: HIV Tat-specific factor 1
+Macromolecule #8: Splicing factor 3B subunit 1
+Macromolecule #9: Probable ATP-dependent RNA helicase DDX46
+Macromolecule #5: U2 snRNA
+Macromolecule #10: ZINC ION
+Macromolecule #11: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.9 Component:
Details: Sample after desalting may have also contained up to 5% glycerol. | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 15531 / Average exposure time: 1.0 sec. / Average electron dose: 53.45 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: RECIPROCAL | ||||||||||||||
Output model | PDB-7q3l: |