+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19041 | |||||||||
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Title | Structure of the human 20S U5 snRNP | |||||||||
Map data | 20S U5 snRNP local filtered map | |||||||||
Sample |
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Keywords | snRNP / CD2BP2 / spliceosome / U5 / 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 / snRNP binding / sno(s)RNA-containing ribonucleoprotein complex / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / 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 / RNA processing / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / Cajal body / 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 / fibrillar center / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / snRNP Assembly / protein-macromolecule adaptor activity / cellular response to lipopolysaccharide / SARS-CoV-2 modulates host translation machinery / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / GTP binding / chromatin / 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: 3.2 Å | |||||||||
Authors | Schneider S / Galej WP | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structure of the human 20S U5 snRNP. Authors: Sarah Schneider / Irina Brandina / Daniel Peter / Sonal Lagad / Angelique Fraudeau / Júlia Portell-Montserrat / Jonas Tholen / Jiangfeng Zhao / Wojciech P Galej / Abstract: The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. ...The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. CD2BP2 is a hallmark protein of the 20S U5 snRNP, absent from the mature tri-snRNP. Here we report a high-resolution cryogenic electron microscopy structure of the 20S U5 snRNP, shedding light on the mutually exclusive interfaces utilized during tri-snRNP assembly and the role of the CD2BP2 in facilitating this process. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19041.map.gz | 8.8 MB | EMDB map data format | |
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Header (meta data) | emd-19041-v30.xml emd-19041.xml | 39.2 KB 39.2 KB | Display Display | EMDB header |
Images | emd_19041.png | 44.1 KB | ||
Filedesc metadata | emd-19041.cif.gz | 12.8 KB | ||
Others | emd_19041_half_map_1.map.gz emd_19041_half_map_2.map.gz | 452.6 MB 452.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19041 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19041 | HTTPS FTP |
-Validation report
Summary document | emd_19041_validation.pdf.gz | 797.9 KB | Display | EMDB validaton report |
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Full document | emd_19041_full_validation.pdf.gz | 797.5 KB | Display | |
Data in XML | emd_19041_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_19041_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19041 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19041 | HTTPS FTP |
-Related structure data
Related structure data | 8rc0MC 8q91C 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_19041.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | 20S U5 snRNP local filtered map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: halfA map
File | emd_19041_half_map_1.map | ||||||||||||
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Annotation | halfA map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfB map
File | emd_19041_half_map_2.map | ||||||||||||
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Annotation | halfB map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 20S U5 snRNP complex purified from HEK293F cell line
+Supramolecule #1: 20S U5 snRNP complex purified from HEK293F cell line
+Macromolecule #1: CD2 antigen cytoplasmic tail-binding protein 2
+Macromolecule #2: Pre-mRNA-processing-splicing factor 8
+Macromolecule #4: Pre-mRNA-processing factor 6
+Macromolecule #5: Probable ATP-dependent RNA helicase DDX23
+Macromolecule #6: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #7: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #8: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #9: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #10: Small nuclear ribonucleoprotein E
+Macromolecule #11: Small nuclear ribonucleoprotein F
+Macromolecule #12: Small nuclear ribonucleoprotein G
+Macromolecule #13: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #14: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #15: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #3: U5 snRNA
+Macromolecule #16: 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: 7.8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Details | objective aperture 70 um |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8506 / Average exposure time: 5.2 sec. / Average electron dose: 40.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 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
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8rc0: |