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- EMDB-0692: Cryo-EM structure of the yeast B*-b2 complex at an average resolu... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0692 | ||||||||||||
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Title | Cryo-EM structure of the yeast B*-b2 complex at an average resolution of 3.7 angstrom | ||||||||||||
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Function / homology | ![]() post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / cellular bud site selection / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) ...post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / cellular bud site selection / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / Prp19 complex / snRNP binding / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / Formation of TC-NER Pre-Incision Complex / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication origin binding / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / Dual incision in TC-NER / DNA replication initiation / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / positive regulation of cell cycle / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / nuclear periphery / RNA splicing / positive regulation of RNA splicing / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / DNA repair / GTPase activity / mRNA binding / chromatin binding / chromatin / GTP binding / mitochondrion / DNA binding / RNA binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
![]() | Wan R / Bai R / Yan C / Lei J / Shi Y | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Authors: Ruixue Wan / Rui Bai / Chuangye Yan / Jianlin Lei / Yigong Shi / ![]() Abstract: Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B) is pivotal for understanding the branching reaction. In this study, we ...Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B) is pivotal for understanding the branching reaction. In this study, we assembled the B complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 221.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 49.7 KB 49.7 KB | Display Display | ![]() |
Images | ![]() | 68.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j6qMC ![]() 0684C ![]() 0685C ![]() 0686C ![]() 0687C ![]() 0691C ![]() 6j6gC ![]() 6j6hC ![]() 6j6nC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : catalytically activated spliceosome B*-a2 complex
+Supramolecule #1: catalytically activated spliceosome B*-a2 complex
+Macromolecule #1: Pre-mRNA-splicing factor 8
+Macromolecule #2: Pre-mRNA-splicing factor SNU114
+Macromolecule #3: Pre-mRNA-splicing factor CWC21
+Macromolecule #4: Pre-mRNA-splicing factor PRP46
+Macromolecule #5: Pre-mRNA-processing protein 45
+Macromolecule #6: Pre-mRNA-splicing factor SLT11
+Macromolecule #7: Pre-mRNA-splicing factor CWC2
+Macromolecule #8: Pre-mRNA-splicing factor CWC15
+Macromolecule #9: Pre-mRNA-splicing factor BUD31
+Macromolecule #10: Pre-mRNA-splicing factor CWC22
+Macromolecule #11: Pre-mRNA-splicing factor CEF1
+Macromolecule #12: Pre-mRNA-splicing factor CLF1
+Macromolecule #13: Pre-mRNA-splicing factor SYF2
+Macromolecule #14: Pre-mRNA-processing factor 17
+Macromolecule #15: Pre-mRNA-splicing factor ISY1
+Macromolecule #20: Pre-mRNA-splicing factor SYF1
+Macromolecule #21: U2 small nuclear ribonucleoprotein B''
+Macromolecule #22: U2 small nuclear ribonucleoprotein A'
+Macromolecule #23: Pre-mRNA-splicing factor SNT309
+Macromolecule #24: Small nuclear ribonucleoprotein E
+Macromolecule #25: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #26: Small nuclear ribonucleoprotein G
+Macromolecule #27: Small nuclear ribonucleoprotein F
+Macromolecule #28: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #29: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #30: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #31: Pre-mRNA-processing factor 19
+Macromolecule #32: Splicing factor YJU2
+Macromolecule #16: UBC4 pre-mRNA
+Macromolecule #17: U5 snRNA
+Macromolecule #18: U6 snRNA
+Macromolecule #19: U2 snRNA
+Macromolecule #33: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #34: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #35: MAGNESIUM ION
+Macromolecule #36: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.9 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 49.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |