+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11569 | |||||||||
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Title | Human C Complex Spliceosome - High-resolution CORE | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information striated muscle dense body / post-spliceosomal complex / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / generation of catalytic spliceosome for first transesterification step / regulation of vitamin D receptor signaling pathway / embryonic brain development / nuclear retinoic acid receptor binding / Prp19 complex ...striated muscle dense body / post-spliceosomal complex / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / generation of catalytic spliceosome for first transesterification step / regulation of vitamin D receptor signaling pathway / embryonic brain development / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / mRNA 3'-end processing / RNA splicing, via transesterification reactions / pre-mRNA binding / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / Notch binding / positive regulation of mRNA splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / muscle organ development / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / Cajal body / positive regulation of neurogenesis / cyclosporin A binding / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of G1/S transition of mitotic cell cycle / retinoic acid receptor signaling pathway / Notch-HLH transcription pathway / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / SMAD binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / mRNA 3'-splice site recognition / protein peptidyl-prolyl isomerization / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNA binding / U5 snRNP / U2 snRNA binding / RNA processing / U6 snRNA binding / pre-mRNA intronic binding / cellular response to retinoic acid / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of RNA splicing / positive regulation of protein export from nucleus / nuclear receptor coactivator activity / DNA damage checkpoint signaling / response to cocaine / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / spliceosomal complex / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / fibrillar center / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Z disc / nuclear matrix / mRNA splicing, via spliceosome / actin filament binding / Dual incision in TC-NER / positive regulation of protein import into nucleus / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA processing / cellular response to xenobiotic stimulus / rRNA processing / transcription corepressor activity / calcium-dependent protein binding / disordered domain specific binding / protein folding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Bertram K / Kastner B | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Mol Cell / Year: 2020 Title: Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome. Authors: Karl Bertram / Leyla El Ayoubi / Olexandr Dybkov / Dmitry E Agafonov / Cindy L Will / Klaus Hartmuth / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / Abstract: Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core ...Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core resolution and 4.5-5.7 Å at its periphery, and aided by protein crosslinking we determine its molecular architecture. Our structure provides additional insights into the spliceosome's architecture between the catalytic steps of splicing, and how proteins aid formation of the spliceosome's catalytically active RNP (ribonucleoprotein) conformation. It reveals the spatial organization of the metazoan-specific proteins PPWD1, WDR70, FRG1, and CIR1 in human C complexes, indicating they stabilize functionally important protein domains and RNA structures rearranged/repositioned during the B to C transition. Structural comparisons with human B, C, and P complexes reveal an intricate cascade of RNP rearrangements during splicing catalysis, with intermediate RNP conformations not found in yeast, and additionally elucidate the structural basis for the sequential recruitment of metazoan-specific spliceosomal proteins. | |||||||||
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_11569.map.gz | 300.6 MB | EMDB map data format | |
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Header (meta data) | emd-11569-v30.xml emd-11569.xml | 45.8 KB 45.8 KB | Display Display | EMDB header |
Images | emd_11569.png | 181.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11569 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11569 | HTTPS FTP |
-Validation report
Summary document | emd_11569_validation.pdf.gz | 261.5 KB | Display | EMDB validaton report |
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Full document | emd_11569_full_validation.pdf.gz | 260.6 KB | Display | |
Data in XML | emd_11569_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11569 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11569 | HTTPS FTP |
-Related structure data
Related structure data | 6zymMC 7a5pC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11569.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Human C complex Spliceosome - High resolution core
+Supramolecule #1: Human C complex Spliceosome - High resolution core
+Macromolecule #1: U2 snRNA
+Macromolecule #2: U5 snRNA
+Macromolecule #3: U6 snRNA
+Macromolecule #19: pre-mRNA
+Macromolecule #4: Corepressor interacting with RBPJ 1
+Macromolecule #5: Pre-mRNA-processing-splicing factor 8
+Macromolecule #6: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #7: SNW domain-containing protein 1
+Macromolecule #8: Pleiotropic regulator 1
+Macromolecule #9: Pre-mRNA-processing factor 17
+Macromolecule #10: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #11: Cell division cycle 5-like protein
+Macromolecule #12: Crooked neck-like protein 1
+Macromolecule #13: Pre-mRNA-splicing factor RBM22
+Macromolecule #14: Protein BUD31 homolog
+Macromolecule #15: Spliceosome-associated protein CWC15 homolog
+Macromolecule #16: Serine/arginine repetitive matrix protein 2
+Macromolecule #17: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #18: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #20: WD repeat-containing protein 70
+Macromolecule #21: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
+Macromolecule #22: Pre-mRNA-splicing factor ISY1 homolog
+Macromolecule #23: Pre-mRNA-splicing factor CWC25 homolog
+Macromolecule #24: Splicing factor YJU2
+Macromolecule #25: Protein FRG1
+Macromolecule #26: MAGNESIUM ION
+Macromolecule #27: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #28: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #29: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 7.9 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II | ||||||||||||
Details | Monodisperse particle distribution |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 28279 / Average exposure time: 1.0 sec. / Average electron dose: 120.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.003 µm / Nominal defocus min: -0.001 µm / Nominal magnification: 132000 |
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
Particle selection | Number selected: 1751359 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 411539 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |