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Yorodumi- EMDB-4364: Prespliceosome structure provides insight into spliceosome assemb... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4364 | |||||||||
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Title | Prespliceosome structure provides insight into spliceosome assembly and regulation (map A2) | |||||||||
Map data | Sharpened A2 map | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of RNA binding / splicing factor binding / mRNA splice site recognition / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome ...positive regulation of RNA binding / splicing factor binding / mRNA splice site recognition / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / positive regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / commitment complex / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / pre-mRNA 5'-splice site binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / response to xenobiotic stimulus / mRNA binding / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Plaschka C / Lin P-C / Charenton C / Nagai K | |||||||||
Citation | Journal: Nature / Year: 2018 Title: Prespliceosome structure provides insights into spliceosome assembly and regulation. Authors: Clemens Plaschka / Pei-Chun Lin / Clément Charenton / Kiyoshi Nagai / Abstract: The spliceosome catalyses the excision of introns from pre-mRNA in two steps, branching and exon ligation, and is assembled from five small nuclear ribonucleoprotein particles (snRNPs; U1, U2, U4, ...The spliceosome catalyses the excision of introns from pre-mRNA in two steps, branching and exon ligation, and is assembled from five small nuclear ribonucleoprotein particles (snRNPs; U1, U2, U4, U5, U6) and numerous non-snRNP factors. For branching, the intron 5' splice site and the branch point sequence are selected and brought by the U1 and U2 snRNPs into the prespliceosome, which is a focal point for regulation by alternative splicing factors. The U4/U6.U5 tri-snRNP subsequently joins the prespliceosome to form the complete pre-catalytic spliceosome. Recent studies have revealed the structural basis of the branching and exon-ligation reactions, however, the structural basis of the early events in spliceosome assembly remains poorly understood. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae prespliceosome at near-atomic resolution. The structure reveals an induced stabilization of the 5' splice site in the U1 snRNP, and provides structural insights into the functions of the human alternative splicing factors LUC7-like (yeast Luc7) and TIA-1 (yeast Nam8), both of which have been linked to human disease. In the prespliceosome, the U1 snRNP associates with the U2 snRNP through a stable contact with the U2 3' domain and a transient yeast-specific contact with the U2 SF3b-containing 5' region, leaving its tri-snRNP-binding interface fully exposed. The results suggest mechanisms for 5' splice site transfer to the U6 ACAGAGA region within the assembled spliceosome and for its subsequent conversion to the activation-competent B-complex spliceosome. Taken together, the data provide a working model to investigate the early steps of spliceosome assembly. | |||||||||
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_4364.map.gz | 627.1 MB | EMDB map data format | |
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Header (meta data) | emd-4364-v30.xml emd-4364.xml | 48.3 KB 48.3 KB | Display Display | EMDB header |
Images | emd_4364.png | 34.8 KB | ||
Others | emd_4364_additional.map.gz | 613.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4364 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4364 | HTTPS FTP |
-Related structure data
Related structure data | 6g90MC 4363C 4365C 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_4364.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened A2 map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened A2 map
File | emd_4364_additional.map | ||||||||||||
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Annotation | Unsharpened A2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Prespliceosome A complex
+Supramolecule #1: Prespliceosome A complex
+Macromolecule #1: U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA
+Macromolecule #2: U2 snRNA
+Macromolecule #11: Yeast UBC4 pre-mRNA (mutant)
+Macromolecule #3: U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleop...
+Macromolecule #4: U1 small nuclear ribonucleoprotein 70 kDa homolog,U1 small nuclea...
+Macromolecule #5: U1 small nuclear ribonucleoprotein C
+Macromolecule #6: Pre-mRNA-processing factor 39
+Macromolecule #7: U1 small nuclear ribonucleoprotein component PRP42
+Macromolecule #8: Protein NAM8
+Macromolecule #9: 56 kDa U1 small nuclear ribonucleoprotein component
+Macromolecule #10: Protein LUC7,Protein LUC7,Protein LUC7
+Macromolecule #12: U1 small nuclear ribonucleoprotein component SNU71
+Macromolecule #13: U2 snRNP component HSH155
+Macromolecule #14: Pre-mRNA-splicing factor RSE1
+Macromolecule #15: Cold sensitive U2 snRNA suppressor 1
+Macromolecule #16: Protein HSH49
+Macromolecule #17: Pre-mRNA-splicing factor RDS3
+Macromolecule #18: Pre-mRNA-splicing factor PRP9
+Macromolecule #19: Pre-mRNA-splicing factor PRP11,Pre-mRNA-splicing factor PRP11,Pre...
+Macromolecule #20: Pre-mRNA-splicing factor PRP21
+Macromolecule #21: U2 small nuclear ribonucleoprotein A'
+Macromolecule #22: Unknown
+Macromolecule #23: U2 small nuclear ribonucleoprotein B''
+Macromolecule #24: RDS3 complex subunit 10
+Macromolecule #25: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #26: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #27: Small nuclear ribonucleoprotein E
+Macromolecule #28: Small nuclear ribonucleoprotein F
+Macromolecule #29: Small nuclear ribonucleoprotein G
+Macromolecule #30: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #31: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #32: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.9 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III Details: Grids were blotted for 2-3.5 s and vitrified by plunging into liquid ethane with a FEI Vitrobot Mark III operated at 4 degree Celsius and 100% humidity.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 9407 / Average electron dose: 43.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Startup model | Type of model: OTHER Details: The initial model was generated from 22319 particles using cryoSPARC. |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 153556 |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6g90: |