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Yorodumi- EMDB-9647: Cryo-EM structure of a human intron lariat spliceosome after Prp4... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9647 | |||||||||
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Title | Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) at 2.9 angstrom resolution | |||||||||
Map data | The 2.86 angstrom map of human ILS2 complex | |||||||||
Sample |
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Function / homology | Function and homology information post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / regulation of vitamin D receptor signaling pathway ...post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / regulation of vitamin D receptor signaling pathway / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / embryonic brain development / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / pre-mRNA binding / ATP-dependent activity, acting on RNA / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / P granule / response to alkaloid / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / positive regulation of mRNA splicing, via spliceosome / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / commitment complex / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / nuclear vitamin D receptor binding / U4 snRNP / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / lipid biosynthetic process / cyclosporin A binding / precatalytic spliceosome / spliceosomal complex assembly / Notch-HLH transcription pathway / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / mitotic G2 DNA damage checkpoint signaling / protein K63-linked ubiquitination / blastocyst development / antiviral innate immune response / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / gastrulation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / positive regulation of G1/S transition of mitotic cell cycle / transcription-coupled nucleotide-excision repair / U5 snRNA binding / U5 snRNP / embryonic organ development / positive regulation of viral genome replication / RNA processing / U2 snRNA binding / Cajal body / U6 snRNA binding / spliceosomal snRNP assembly / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / cellular response to retinoic acid / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / lipid droplet Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Zhang X / Zhan X / Yan C / Shi Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Res / Year: 2019 Title: Structures of the human spliceosomes before and after release of the ligated exon. Authors: Xiaofeng Zhang / Xiechao Zhan / Chuangye Yan / Wenyu Zhang / Dongliang Liu / Jianlin Lei / Yigong Shi / Abstract: Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ...Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3'-splice site is recognized by the junction between the 5'-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome disassembly. | |||||||||
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_9647.map.gz | 226.6 MB | EMDB map data format | |
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Header (meta data) | emd-9647-v30.xml emd-9647.xml | 51.3 KB 51.3 KB | Display Display | EMDB header |
Images | emd_9647.png | 86.1 KB | ||
Others | emd_9647_additional.map.gz | 193.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9647 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9647 | HTTPS FTP |
-Related structure data
Related structure data | 6id1MC 9645C 9646C 6iczC 6id0C 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_9647.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The 2.86 angstrom map of human ILS2 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.338 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: The 4.0 angstrom map of the human ILS2 complex
File | emd_9647_additional.map | ||||||||||||
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Annotation | The 4.0 angstrom map of the human ILS2 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human Intron Lariat Spliceosome
+Supramolecule #1: Human Intron Lariat Spliceosome
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #3: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #4: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #6: Crooked neck-like protein 1
+Macromolecule #7: Cell division cycle 5-like protein
+Macromolecule #8: Pre-mRNA-splicing factor SYF2
+Macromolecule #9: Protein BUD31 homolog
+Macromolecule #10: Pre-mRNA-splicing factor RBM22
+Macromolecule #11: Spliceosome-associated protein CWC15 homolog
+Macromolecule #12: SNW domain-containing protein 1
+Macromolecule #13: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #14: Pleiotropic regulator 1
+Macromolecule #15: Pre-mRNA-processing factor 17
+Macromolecule #18: CWF19-like protein 2
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #20: Small nuclear ribonucleoprotein-associated protein
+Macromolecule #21: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #22: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #23: Small nuclear ribonucleoprotein F
+Macromolecule #24: Small nuclear ribonucleoprotein E
+Macromolecule #25: Small nuclear ribonucleoprotein G
+Macromolecule #26: Pre-mRNA-processing factor 19
+Macromolecule #27: Pre-mRNA-splicing factor SPF27
+Macromolecule #28: Pre-mRNA-splicing factor SYF1
+Macromolecule #29: RNA helicase aquarius
+Macromolecule #30: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #31: U2 small nuclear ribonucleoprotein A'
+Macromolecule #32: U2 small nuclear ribonucleoprotein B''
+Macromolecule #33: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
+Macromolecule #2: U5snRNA
+Macromolecule #5: U6snRNA
+Macromolecule #16: pre-mRNA
+Macromolecule #17: U2snRNA
+Macromolecule #34: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #35: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: 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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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: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 499840 |