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Yorodumi- EMDB-9645: Cryo-EM structure of a human post-catalytic spliceosome (P comple... -
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-Basic information
Entry | Database: EMDB / ID: EMD-9645 | |||||||||
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Title | Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom | |||||||||
Map data | The 3.0 angstrom map of the human P complex | |||||||||
Sample |
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Function / homology | Function and homology information second spliceosomal transesterification activity / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / spliceosomal complex disassembly / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / pre-mRNA 3'-splice site binding / snRNP binding ...second spliceosomal transesterification activity / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / spliceosomal complex disassembly / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / pre-mRNA 3'-splice site binding / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / intracellular mRNA localization / histone pre-mRNA DCP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNP / 3'-5' RNA helicase activity / regulation of translation at postsynapse, modulating synaptic transmission / histone pre-mRNA 3'end processing complex / alternative mRNA splicing, via spliceosome / renal system process / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / negative regulation of excitatory postsynaptic potential / regulation of vitamin D receptor signaling pathway / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / Deadenylation of mRNA / embryonic brain development / protein methylation / U12-type spliceosomal complex / methylosome / negative regulation of phosphorylation / 7-methylguanosine cap hypermethylation / pre-mRNA binding / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / Prp19 complex / poly(A) binding / positive regulation of androgen receptor activity / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / M-decay: degradation of maternal mRNAs by maternally stored factors / P granule / RNA stem-loop binding / sno(s)RNA-containing ribonucleoprotein complex / ATP-dependent activity, acting on RNA / SMN-Sm protein complex / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / embryonic cranial skeleton morphogenesis / telomerase holoenzyme complex / positive regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / positive regulation by host of viral transcription / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / U2 snRNP / Notch binding / nuclear vitamin D receptor binding / RNA Polymerase II Transcription Termination / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U1 snRNP / RUNX3 regulates NOTCH signaling / U2-type prespliceosome / NOTCH4 Intracellular Domain Regulates Transcription / K63-linked polyubiquitin modification-dependent protein binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ubiquitin-ubiquitin ligase activity / exploration behavior / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / lipid biosynthetic process / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / protein kinase inhibitor activity / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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_9645.map.gz | 226.9 MB | EMDB map data format | |
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Header (meta data) | emd-9645-v30.xml emd-9645.xml | 65.1 KB 65.1 KB | Display Display | EMDB header |
Images | emd_9645.png | 89.7 KB | ||
Others | emd_9645_additional.map.gz | 193.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9645 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9645 | HTTPS FTP |
-Related structure data
Related structure data | 6iczMC 9646C 9647C 6id0C 6id1C 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_9645.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The 3.0 angstrom map of the human P complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 4.7 angstrom map of the human P complex
File | emd_9645_additional.map | ||||||||||||
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Annotation | The 4.7 angstrom map of the human P complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human Post_catalytic Spliceosome
+Supramolecule #1: Human Post_catalytic Spliceosome
+Macromolecule #1: Protein mago nashi homolog 2
+Macromolecule #2: RNA-binding protein 8A
+Macromolecule #3: Eukaryotic initiation factor 4A-III
+Macromolecule #4: Protein CASC3
+Macromolecule #5: Pre-mRNA-processing-splicing factor 8
+Macromolecule #7: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #8: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #12: Crooked neck-like protein 1
+Macromolecule #13: Cell division cycle 5-like protein
+Macromolecule #14: Pre-mRNA-splicing factor SYF2
+Macromolecule #15: Protein BUD31 homolog
+Macromolecule #16: Pre-mRNA-splicing factor RBM22
+Macromolecule #17: Spliceosome-associated protein CWC15 homolog
+Macromolecule #18: SNW domain-containing protein 1
+Macromolecule #19: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #20: Pleiotropic regulator 1
+Macromolecule #21: Serine/arginine repetitive matrix protein 2
+Macromolecule #22: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #23: Pre-mRNA-processing factor 17
+Macromolecule #24: PRKR-interacting protein 1
+Macromolecule #25: Pre-mRNA-splicing factor SLU7
+Macromolecule #26: Pre-mRNA-splicing factor SYF1
+Macromolecule #27: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #28: RNA helicase aquarius
+Macromolecule #29: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #30: Small nuclear ribonucleoprotein-associated protein
+Macromolecule #31: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #32: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #33: Small nuclear ribonucleoprotein F
+Macromolecule #34: Small nuclear ribonucleoprotein E
+Macromolecule #35: Small nuclear ribonucleoprotein G
+Macromolecule #36: U2 small nuclear ribonucleoprotein A'
+Macromolecule #37: U2 small nuclear ribonucleoprotein B''
+Macromolecule #38: ATP-dependent RNA helicase DHX8
+Macromolecule #39: Pre-mRNA-splicing factor SPF27
+Macromolecule #40: Pre-mRNA-processing factor 19
+Macromolecule #41: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #6: U5snRNA
+Macromolecule #9: U6snRNA
+Macromolecule #10: pre-mRNA
+Macromolecule #11: U2snRNA
+Macromolecule #42: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #43: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #44: MAGNESIUM ION
+Macromolecule #45: ZINC ION
+Macromolecule #46: ADENOSINE-5'-TRIPHOSPHATE
-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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143320 |