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Yorodumi- EMDB-13029: The U1 part of Saccharomyces cerevisiae spliceosomal pre-A comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13029 | |||||||||
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Title | The U1 part of Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1) | |||||||||
Map data | U1 part of the pre-A complex | |||||||||
Sample |
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Keywords | S. cerevisiae / pre-A complex / Prp5 / U1 snRNP / U2 snRNP / prespliceosome / SPLICING | |||||||||
Function / homology | Function and homology information positive regulation of RNA binding / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / commitment complex ...positive regulation of RNA binding / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / commitment complex / U2-type prespliceosome assembly / poly(U) RNA binding / U4 snRNP / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / U5 snRNP / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / mRNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Zhang Z / Rigo N | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nature / Year: 2021 Title: Structural insights into how Prp5 proofreads the pre-mRNA branch site. Authors: Zhenwei Zhang / Norbert Rigo / Olexandr Dybkov / Jean-Baptiste Fourmann / Cindy L Will / Vinay Kumar / Henning Urlaub / Holger Stark / Reinhard Lührmann / Abstract: During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex-a poorly ...During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex-a poorly understood, multistep process that is facilitated by the DEAD-box helicase Prp5 (refs. ). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2-BS helix), which is proofread by Prp5 at this stage through an unclear mechanism. Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identified assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2-BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. Our data suggest that binding of Hsh155 to the bulged BS-A of the U2-BS helix triggers closure of Hsh155, which in turn destabilizes Prp5 binding. Thus, Prp5 proofreads the branch site indirectly, hindering spliceosome assembly if branch-site mutations prevent the remodelling of Hsh155. Our data provide structural insights into how a spliceosomal helicase enhances the fidelity of pre-mRNA splicing. | |||||||||
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_13029.map.gz | 227.8 MB | EMDB map data format | |
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Header (meta data) | emd-13029-v30.xml emd-13029.xml | 35 KB 35 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13029_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_13029.png | 124.1 KB | ||
Filedesc metadata | emd-13029.cif.gz | 9.5 KB | ||
Others | emd_13029_half_map_1.map.gz emd_13029_half_map_2.map.gz | 170.1 MB 170.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13029 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13029 | HTTPS FTP |
-Validation report
Summary document | emd_13029_validation.pdf.gz | 865.7 KB | Display | EMDB validaton report |
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Full document | emd_13029_full_validation.pdf.gz | 865.3 KB | Display | |
Data in XML | emd_13029_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | emd_13029_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13029 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13029 | HTTPS FTP |
-Related structure data
Related structure data | 7oqcMC 7oqbC 7oqeC 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_13029.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | U1 part of the pre-A complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map 2
File | emd_13029_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map1
File | emd_13029_half_map_2.map | ||||||||||||
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Annotation | half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : S. cerevisiae spliceosomal pre-A complex
+Supramolecule #1: S. cerevisiae spliceosomal pre-A complex
+Macromolecule #1: Protein NAM8
+Macromolecule #3: U1 small nuclear ribonucleoprotein component PRP42
+Macromolecule #4: U1 small nuclear ribonucleoprotein component SNU71
+Macromolecule #6: 56 kDa U1 small nuclear ribonucleoprotein component
+Macromolecule #7: U1 small nuclear ribonucleoprotein A
+Macromolecule #8: U1 small nuclear ribonucleoprotein C
+Macromolecule #9: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #10: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #11: Small nuclear ribonucleoprotein E
+Macromolecule #12: Small nuclear ribonucleoprotein F
+Macromolecule #13: Small nuclear ribonucleoprotein G
+Macromolecule #14: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #15: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #16: Protein LUC7
+Macromolecule #17: Pre-mRNA-processing factor 39
+Macromolecule #18: U1 small nuclear ribonucleoprotein 70 kDa homolog
+Macromolecule #2: ACT1 pre-mRNA (delta BS-A),ACT1 pre-mRNA (delta BS-A),ACT1 pre-mR...
+Macromolecule #5: U1 snRNA
-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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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
-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 / Average exposure time: 1.02 sec. / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |