+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13813 | |||||||||
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Title | A-like U2 snRNP medium-resolution map | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Splicing / snRNP / Spliceosome / NUCLEAR PROTEIN | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13813.map.gz | 97.7 MB | EMDB map data format | |
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Header (meta data) | emd-13813-v30.xml emd-13813.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13813_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_13813.png | 95 KB | ||
Masks | emd_13813_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-13813.cif.gz | 5 KB | ||
Others | emd_13813_half_map_1.map.gz emd_13813_half_map_2.map.gz | 97.9 MB 98.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13813 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13813 | HTTPS FTP |
-Validation report
Summary document | emd_13813_validation.pdf.gz | 190 KB | Display | EMDB validaton report |
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Full document | emd_13813_full_validation.pdf.gz | 189.6 KB | Display | |
Data in XML | emd_13813_validation.xml.gz | 501 B | Display | |
Data in CIF | emd_13813_validation.cif.gz | 373 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13813 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13813 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13813.map.gz / Format: CCP4 / Size: 125 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: 1.28 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_13813_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13813_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13813_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : A-like U2 snRNP
Entire | Name: A-like U2 snRNP |
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Components |
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-Supramolecule #1: A-like U2 snRNP
Supramolecule | Name: A-like U2 snRNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 Details: Spliceosomal complex A-like U2 snRNP generated by binding BPS oligo to 17S U2 snRNP that was isolated from nuclear extract of HEK293F cells by affinity chromatography. |
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Molecular weight | Theoretical: 300 KDa |
-Supramolecule #2: A-like U2 snRNP
Supramolecule | Name: A-like U2 snRNP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#9 Details: Spliceosomal complex A-like U2 snRNP generated by binding BPS oligo to 17S U2 snRNP that was isolated from nuclear extract of HEK293F cells by affinity chromatography. |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: BPS Oligo
Supramolecule | Name: BPS Oligo / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #10 / Details: BPS Oligo |
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Source (natural) | Organism: synthetic construct (others) |
-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 - Time: 60 sec. / 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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Specialist optics | Energy filter - Slit width: 20 eV |
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: 15681 / Average exposure time: 1.0 sec. / Average electron dose: 52.03 e/Å2 |
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 FIELD / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: RECIPROCAL |