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Yorodumi- EMDB-9526: Cryo-EM structure of the Catalytic Step I spliceosome (C complex)... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9526 | |||||||||
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Title | Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.65 angstrom resolution | |||||||||
Map data | Cryo-EM map of Catalytic Step I spliceosome (C complex) at 3.65 angstrom resolution | |||||||||
Sample |
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Function / homology | Function and homology information post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / cellular bud site selection / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U4/U6 snRNP ...post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / cellular bud site selection / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / Prp19 complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / Dual incision in TC-NER / DNA replication origin binding / generation of catalytic spliceosome for second transesterification step / protein K63-linked ubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / DNA replication initiation / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding / positive regulation of cell cycle / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / nuclear periphery / positive regulation of RNA splicing / RNA splicing / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / cell cycle / DNA repair / mRNA binding / GTPase activity / chromatin binding / chromatin / GTP binding / mitochondrion / DNA binding / RNA binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.65 Å | |||||||||
Authors | Wan R / Yan C / Bai R / Huang G / Shi Y | |||||||||
Citation | Journal: Science / Year: 2016 Title: Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution. Authors: Ruixue Wan / Chuangye Yan / Rui Bai / Gaoxingyu Huang / Yigong Shi / Abstract: Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. ...Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. Here we report an atomic structure of a catalytic step I spliceosome (known as the C complex) from Saccharomyces cerevisiae, as determined by cryo-electron microscopy at an average resolution of 3.4 angstroms. In the structure, the 2'-OH of the invariant adenine nucleotide in the branch point sequence (BPS) is covalently joined to the phosphate at the 5' end of the 5' splice site (5'SS), forming an intron lariat. The freed 5' exon remains anchored to loop I of U5 small nuclear RNA (snRNA), and the 5'SS and BPS of the intron form duplexes with conserved U6 and U2 snRNA sequences, respectively. Specific placement of these RNA elements at the catalytic cavity of Prp8 is stabilized by 15 protein components, including Snu114 and the splicing factors Cwc21, Cwc22, Cwc25, and Yju2. These features, representing the conformation of the spliceosome after the first-step reaction, predict structural changes that are needed for the execution of the second-step transesterification reaction. | |||||||||
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_9526.map.gz | 228.7 MB | EMDB map data format | |
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Header (meta data) | emd-9526-v30.xml emd-9526.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | emd_9526.png | 184.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9526 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9526 | HTTPS FTP |
-Related 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_9526.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of Catalytic Step I spliceosome (C complex) at 3.65 angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.306 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 : Catalytic Step I Spliceosome (C complex)
Entire | Name: Catalytic Step I Spliceosome (C complex) |
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Components |
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-Supramolecule #1: Catalytic Step I Spliceosome (C complex)
Supramolecule | Name: Catalytic Step I Spliceosome (C complex) / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 4.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80367 |