+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7109 | ||||||||||||
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Title | S. cerevisiae spliceosomal post-catalytic P complex | ||||||||||||
Map data | Spliceosomal post-catalytic P complex | ||||||||||||
Sample |
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Function / homology | Function and homology information U2-type post-spliceosomal complex / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / spliceosomal complex disassembly / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome ...U2-type post-spliceosomal complex / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / spliceosomal complex disassembly / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / 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 / pICln-Sm protein complex / snRNP binding / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / pre-mRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / 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 / DNA replication origin binding / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / Dual incision in TC-NER / spliceosomal tri-snRNP complex assembly / DNA replication initiation / U5 snRNA binding / positive regulation of cell cycle / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / nuclear periphery / 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 / RNA helicase activity / RNA helicase / DNA repair / GTPase activity / mRNA binding / chromatin binding / GTP binding / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / metal ion binding / 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: 3.3 Å | ||||||||||||
Authors | Liu S / Li X / Zhou ZH / Zhao R | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Science / Year: 2017 Title: Structure of the yeast spliceosomal postcatalytic P complex. Authors: Shiheng Liu / Xueni Li / Lingdi Zhang / Jiansen Jiang / Ryan C Hill / Yanxiang Cui / Kirk C Hansen / Z Hong Zhou / Rui Zhao / Abstract: The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B, C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, ...The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B, C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, and intron release, but lacked information on 3'-ss recognition, exon ligation, and exon release. Here we report a cryo-electron microscopy structure of the postcatalytic P complex at 3.3-angstrom resolution, revealing that the 3' ss is mainly recognized through non-Watson-Crick base pairing with the 5' ss and branch point. Furthermore, one or more unidentified proteins become stably associated with the P complex, securing the 3' exon and potentially regulating activity of the helicase Prp22. Prp22 binds nucleotides 15 to 21 in the 3' exon, enabling it to pull the intron-exon or ligated exons in a 3' to 5' direction to achieve 3'-ss proofreading or exon release, respectively. | ||||||||||||
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_7109.map.gz | 227.2 MB | EMDB map data format | |
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Header (meta data) | emd-7109-v30.xml emd-7109.xml | 55.9 KB 55.9 KB | Display Display | EMDB header |
Images | emd_7109.png | 68.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7109 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7109 | HTTPS FTP |
-Validation report
Summary document | emd_7109_validation.pdf.gz | 512.7 KB | Display | EMDB validaton report |
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Full document | emd_7109_full_validation.pdf.gz | 512.3 KB | Display | |
Data in XML | emd_7109_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_7109_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7109 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7109 | HTTPS FTP |
-Related structure data
Related structure data | 6bk8MC 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_7109.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Spliceosomal post-catalytic P complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 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 : Spliceosomal P complex
+Supramolecule #1: Spliceosomal P complex
+Macromolecule #1: U2 snRNA
+Macromolecule #2: U5 snRNA
+Macromolecule #3: U6 snRNA
+Macromolecule #4: RNA (34-MER)
+Macromolecule #5: RNA (59-MER)
+Macromolecule #6: Pre-mRNA-splicing factor Prp8
+Macromolecule #7: Pre-mRNA-splicing factor SNU114
+Macromolecule #8: Pre-mRNA-splicing factor PRP46
+Macromolecule #9: Pre-mRNA-processing protein 45
+Macromolecule #10: Pre-mRNA-splicing factor SLT11
+Macromolecule #11: Pre-mRNA-splicing factor CWC2
+Macromolecule #12: Pre-mRNA-splicing factor CWC15
+Macromolecule #13: Pre-mRNA-splicing factor BUD31
+Macromolecule #14: Pre-mRNA-splicing factor CWC21
+Macromolecule #15: Pre-mRNA-splicing factor CWC22
+Macromolecule #16: Pre-mRNA-processing factor Prp17
+Macromolecule #17: Pre-mRNA-splicing factor Prp18
+Macromolecule #18: Pre-mRNA-splicing factor SLU7
+Macromolecule #19: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22
+Macromolecule #20: Pre-mRNA-splicing factor SYF2
+Macromolecule #21: Pre-mRNA-splicing factor CEF1
+Macromolecule #22: Pre-mRNA-splicing factor CLF1
+Macromolecule #23: Pre-mRNA-splicing factor SYF1
+Macromolecule #24: Unknown protein fragment
+Macromolecule #25: Unknown protein fragment
+Macromolecule #26: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #27: Small nuclear ribonucleoprotein F
+Macromolecule #28: Small nuclear ribonucleoprotein E
+Macromolecule #29: Small nuclear ribonucleoprotein G
+Macromolecule #30: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #31: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #32: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #33: Lea1
+Macromolecule #34: Msl1
+Macromolecule #35: Pre-mRNA-processing factor Prp19
+Macromolecule #36: Pre-mRNA-splicing factor SNT309
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #39: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #40: ZINC ION
-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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Vitrification | Cryogen name: ETHANE |
-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: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | The author states the following for the pre-mRNA model building: For regions in the intron or exon where no clear sequence preferences were observed (Spingola et al., PMID 10024174), U, A, U, and A-U are used to represent a generic nucleotide, purine, pyrimidine, and standard Watson-Crick basepair, respectively, based on the EM density. Nucleotides -7 to +7 in the exon are modeled mostly as the preferred nucleotides in each position (Spingola et al. PMID 10024174) unless the density suggests otherwise. Some nucleotides in the intron seem to form basepairs with defined U2 or U6 snRNA sequence based on EM densities, and are modeled as complementary nucleotides to the corresponding U2 or U6 sequence unless the density suggests otherwise. |
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Output model | PDB-6bk8: |