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Yorodumi- EMDB-18235: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (St... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18235 | |||||||||
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Title | Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 3, Map 3) | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Keywords | U5 snRNP / CD2BP2 / TSSC4 / spliceosome / splicing | |||||||||
Function / homology | Function and homology information RNA localization / R-loop processing / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs ...RNA localization / R-loop processing / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / sno(s)RNA-containing ribonucleoprotein complex / snRNP binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / Cajal body / RNA processing / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / fibrillar center / mRNA processing / osteoblast differentiation / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / snRNP Assembly / protein-macromolecule adaptor activity / SARS-CoV-2 modulates host translation machinery / cellular response to lipopolysaccharide / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / chromatin / GTP binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 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_18235.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-18235-v30.xml emd-18235.xml | 37.6 KB 37.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18235_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_18235.png | 69.2 KB | ||
Filedesc metadata | emd-18235.cif.gz | 12.2 KB | ||
Others | emd_18235_additional_1.map.gz emd_18235_half_map_1.map.gz emd_18235_half_map_2.map.gz | 89.5 MB 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18235 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18235 | HTTPS FTP |
-Validation report
Summary document | emd_18235_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_18235_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_18235_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | emd_18235_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18235 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18235 | HTTPS FTP |
-Related structure data
Related structure data | 8q7wMC 8q7qC 8q7vC 8q7xC C: citing same article (ref.) M: atomic model generated by this map |
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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_18235.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_18235_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_18235_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_18235_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 (St...
+Supramolecule #1: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (St...
+Macromolecule #1: U5 snRNA
+Macromolecule #2: Pre-mRNA-processing-splicing factor 8
+Macromolecule #3: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #5: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #6: Probable ATP-dependent RNA helicase DDX23
+Macromolecule #7: Pre-mRNA-processing factor 6
+Macromolecule #8: CD2 antigen cytoplasmic tail-binding protein 2
+Macromolecule #9: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #10: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #11: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #12: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #13: Small nuclear ribonucleoprotein E
+Macromolecule #14: Small nuclear ribonucleoprotein F
+Macromolecule #15: Small nuclear ribonucleoprotein G
+Macromolecule #16: MAGNESIUM ION
+Macromolecule #17: GUANOSINE-5'-TRIPHOSPHATE
-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 |