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Yorodumi- EMDB-6817: Cryo-EM structure of the intron-lariat spliceosome ready for disa... -
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-Basic information
Entry | Database: EMDB / ID: EMD-6817 | |||||||||
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Title | Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom | |||||||||
Map data | Cryo-EM map of the ILS spliceosome from S.cerevisiae at 3.5 angstrom | |||||||||
Sample |
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Keywords | ILS complex / Ntr complex / disassembly / Prp43 / SPLICING | |||||||||
Function / homology | Function and homology information negative regulation of DNA ligase activity / negative regulation of double-strand break repair via nonhomologous end joining / U2-type post-mRNA release spliceosomal complex / spliceosomal complex disassembly / 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 ...negative regulation of DNA ligase activity / negative regulation of double-strand break repair via nonhomologous end joining / U2-type post-mRNA release spliceosomal complex / spliceosomal complex disassembly / 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 / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / commitment complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / poly(U) RNA binding / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / Formation of TC-NER Pre-Incision Complex / generation of catalytic spliceosome for second transesterification step / DNA replication origin binding / Gap-filling DNA repair synthesis and ligation in TC-NER / protein K63-linked ubiquitination / mRNA 5'-splice site recognition / regulation of RNA splicing / mRNA 3'-splice site recognition / Dual incision in TC-NER / spliceosomal tri-snRNP complex assembly / DNA replication initiation / U5 snRNA binding / U5 snRNP / negative regulation of protein-containing complex assembly / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / positive regulation of cell cycle / pre-mRNA intronic binding / 90S preribosome / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / catalytic step 2 spliceosome / nuclear periphery / RNA splicing / positive regulation of RNA splicing / ribosomal large subunit biogenesis / helicase activity / maturation of SSU-rRNA / negative regulation of protein binding / small-subunit processome / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / rRNA processing / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / nucleic acid binding / chromosome, telomeric region / RNA helicase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / cell cycle / DNA repair / GTPase activity / mRNA binding / chromatin binding / chromatin / nucleolus / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Wan R / Yan C | |||||||||
Citation | Journal: Cell / Year: 2017 Title: Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae. Authors: Ruixue Wan / Chuangye Yan / Rui Bai / Jianlin Lei / Yigong Shi / Abstract: The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an ...The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an average resolution of 3.5 Å. The intron lariat remains bound in the spliceosome whereas the ligated exon is already dissociated. The step II splicing factors Prp17 and Prp18, along with Cwc21 and Cwc22 that stabilize the 5' exon binding to loop I of U5 small nuclear RNA (snRNA), have been released from the active site assembly. The DEAH family ATPase/helicase Prp43 binds Syf1 at the periphery of the spliceosome, with its RNA-binding site close to the 3' end of U6 snRNA. The C-terminal domain of Ntr1/Spp382 associates with the GTPase Snu114, and Ntr2 is anchored to Prp8 while interacting with the superhelical domain of Ntr1. These structural features suggest a plausible mechanism for the disassembly of the ILS complex. | |||||||||
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_6817.map.gz | 227.5 MB | EMDB map data format | |
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Header (meta data) | emd-6817-v30.xml emd-6817.xml | 59.7 KB 59.7 KB | Display Display | EMDB header |
Images | emd_6817.png | 86 KB | ||
Filedesc metadata | emd-6817.cif.gz | 15.5 KB | ||
Others | emd_6817_additional_1.map.gz emd_6817_additional_2.map.gz | 4.5 MB 192.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6817 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6817 | HTTPS FTP |
-Related structure data
Related structure data | 5y88MC 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_6817.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 the ILS spliceosome from S.cerevisiae at 3.5 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Additional map: local map for the Prp43 region of the...
File | emd_6817_additional_1.map | ||||||||||||
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Annotation | local map for the Prp43 region of the ILS spliceosome from S.cerevisiae | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: local map for the Spp382 region of the...
File | emd_6817_additional_2.map | ||||||||||||
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Annotation | local map for the Spp382 region of the ILS spliceosome from S.cerevisiae | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : S. cerevisiae intron lariat spliceosome (ILS)
+Supramolecule #1: S. cerevisiae intron lariat spliceosome (ILS)
+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-splicing factor SLT11
+Macromolecule #14: Pre-mRNA-splicing factor CWC2
+Macromolecule #15: Pre-mRNA-splicing factor PRP46
+Macromolecule #16: Pre-mRNA-splicing factor CWC15
+Macromolecule #17: Pre-mRNA-processing protein 45
+Macromolecule #18: Protein CWC16
+Macromolecule #19: Pre-mRNA-processing factor 17
+Macromolecule #20: Pre-mRNA-splicing factor CWC23
+Macromolecule #21: Pre-mRNA-splicing factor SPP382
+Macromolecule #22: Pre-mRNA-splicing factor NTR2
+Macromolecule #23: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
+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: Intron lariat
+Macromolecule #6: U2 snRNA
+Macromolecule #34: RNA (intron or U6 snRNA)
+Macromolecule #35: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #36: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: ZINC ION
-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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Grid | Model: GLOW DISCHARGE |
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 / Cs: 2.7 mm |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 37.6 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: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.0) |
Final 3D classification | Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 150363 |