[English] 日本語
Yorodumi- EMDB-6839: Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6839 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom | ||||||||||||
Map data | Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom | ||||||||||||
Sample |
| ||||||||||||
Keywords | Post-catalytic Spliceosome (P complex) / RNA splicing / exon ligation / spliceosome / SPLICING | ||||||||||||
Function / homology | Function and homology information U2-type post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / spliceosomal complex disassembly / mRNA branch site recognition / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / nuclear mRNA surveillance ...U2-type post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / spliceosomal complex disassembly / mRNA branch site recognition / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / nuclear mRNA surveillance / 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 / Gap-filling DNA repair synthesis and ligation in TC-NER / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / DNA replication initiation / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / spliceosomal snRNP assembly / U2 snRNA binding / 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 / 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 / cell cycle / DNA repair / mRNA binding / GTPase activity / chromatin binding / chromatin / GTP binding / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP 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: 3.6 Å | ||||||||||||
Authors | Wan R / Yan C | ||||||||||||
Funding support | China, 3 items
| ||||||||||||
Citation | Journal: Cell / Year: 2017 Title: Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae. Authors: Rui Bai / Chuangye Yan / Ruixue Wan / Jianlin Lei / Yigong Shi / Abstract: Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the ...Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3.6 Å. The ligated exon is held in the active site through RNA-RNA contacts. Three bases at the 3' end of the 5' exon remain anchored to loop I of U5 small nuclear RNA, and the conserved AG nucleotides of the 3'-splice site (3'SS) are specifically recognized by the invariant adenine of the branch point sequence, the guanine base at the 5' end of the 5'SS, and an adenine base of U6 snRNA. The 3'SS is stabilized through an interaction with the 1585-loop of Prp8. The P complex structure provides a view on splice junction formation critical for understanding the complete splicing cycle. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6839.map.gz | 228.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6839-v30.xml emd-6839.xml | 57.3 KB 57.3 KB | Display Display | EMDB header |
Images | emd_6839.png | 153.3 KB | ||
Filedesc metadata | emd-6839.cif.gz | 15.4 KB | ||
Others | emd_6839_additional.map.gz | 228.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6839 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6839 | HTTPS FTP |
-Related structure data
Related structure data | 5ylzMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6839.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces...
File | emd_6839_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.85 angstrom | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : the Post-catalytic Spliceosome (P complex)
+Supramolecule #1: the Post-catalytic Spliceosome (P complex)
+Macromolecule #1: Pre-mRNA-splicing factor 8
+Macromolecule #3: Pre-mRNA-splicing factor SNU114
+Macromolecule #7: Pre-mRNA-splicing factor SNT309
+Macromolecule #8: Pre-mRNA-splicing factor SYF1
+Macromolecule #9: Pre-mRNA-splicing factor CLF1
+Macromolecule #10: Pre-mRNA-splicing factor CEF1
+Macromolecule #11: Pre-mRNA-splicing factor SYF2
+Macromolecule #12: Pre-mRNA-splicing factor BUD31
+Macromolecule #13: Pre-mRNA-processing factor 17
+Macromolecule #14: Pre-mRNA-splicing factor SLT11
+Macromolecule #15: Pre-mRNA-splicing factor CWC2
+Macromolecule #16: Pre-mRNA-splicing factor PRP46
+Macromolecule #17: Pre-mRNA-splicing factor CWC15
+Macromolecule #18: Pre-mRNA-processing protein 45
+Macromolecule #19: Pre-mRNA-splicing factor CWC21
+Macromolecule #20: Pre-mRNA-splicing factor CWC22
+Macromolecule #21: Pre-mRNA-splicing factor 18
+Macromolecule #22: Pre-mRNA-splicing factor SLU7
+Macromolecule #23: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22
+Macromolecule #24: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #25: Small nuclear ribonucleoprotein E
+Macromolecule #26: Small nuclear ribonucleoprotein F
+Macromolecule #27: Small nuclear ribonucleoprotein G
+Macromolecule #28: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #29: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #30: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #31: U2 small nuclear ribonucleoprotein A'
+Macromolecule #32: U2 small nuclear ribonucleoprotein B''
+Macromolecule #33: Pre-mRNA-processing factor 19
+Macromolecule #2: U5 snRNA
+Macromolecule #4: U6 snRNA
+Macromolecule #5: mRNA/intron lariat
+Macromolecule #6: U2 snRNA
+Macromolecule #34: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #35: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |
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) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final 3D classification | Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 134517 |