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Yorodumi- EMDB-18239: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18239 | |||||||||
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Title | Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and TSSC4 (Map 6) | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Keywords | U5 snRNP / CD2BP2 / TSSC4 / spliceosome / splicing | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Riabov Bassat D / Plaschka C / Vorlaender MK | |||||||||
Funding support | European Union, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural basis of human U5 snRNP late biogenesis and recycling. Authors: Daria Riabov Bassat / Supapat Visanpattanasin / Matthias K Vorländer / Laura Fin / Alexander W Phillips / Clemens Plaschka / Abstract: Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP ...Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP is the ~1 MDa 'heart' of the spliceosome and is recycled through an unknown mechanism involving major architectural rearrangements and the dedicated chaperones CD2BP2 and TSSC4. Late steps in U5 snRNP biogenesis similarly involve these chaperones. Here we report cryo-electron microscopy structures of four human U5 snRNP-CD2BP2-TSSC4 complexes, revealing how a series of molecular events primes the U5 snRNP to generate the ~2 MDa U4/U6.U5 tri-snRNP, the largest building block of the spliceosome. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18239.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-18239-v30.xml emd-18239.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18239_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_18239.png | 49.3 KB | ||
Filedesc metadata | emd-18239.cif.gz | 3.9 KB | ||
Others | emd_18239_additional_1.map.gz emd_18239_half_map_1.map.gz emd_18239_half_map_2.map.gz | 90.2 MB 164.9 MB 164.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18239 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18239 | HTTPS FTP |
-Validation report
Summary document | emd_18239_validation.pdf.gz | 952.8 KB | Display | EMDB validaton report |
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Full document | emd_18239_full_validation.pdf.gz | 952.4 KB | Display | |
Data in XML | emd_18239_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | emd_18239_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18239 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18239 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18239.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpened map
File | emd_18239_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_18239_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_18239_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and...
Entire | Name: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and TSSC4 (Map 6) |
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Components |
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-Supramolecule #1: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and...
Supramolecule | Name: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and TSSC4 (Map 6) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |