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- 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 | |||||||||
![]() | The 3.0 angstrom map of the human P complex | |||||||||
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Function / homology | ![]() 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 / cellular response to selenite ion / spliceosomal complex disassembly / exon-exon junction complex / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway ...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 / cellular response to selenite ion / spliceosomal complex disassembly / exon-exon junction complex / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / regulation of translation at postsynapse, modulating synaptic transmission / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / renal system process / generation of catalytic spliceosome for first transesterification step / intracellular mRNA localization / negative regulation of excitatory postsynaptic potential / U7 snRNP / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / histone pre-mRNA 3'end processing complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / regulation of mRNA processing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / selenocysteine insertion sequence binding / Deadenylation of mRNA / embryonic brain development / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / negative regulation of phosphorylation / methylosome / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / U1 snRNP binding / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-end processing / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / ATP-dependent activity, acting on RNA / small nuclear ribonucleoprotein complex / embryonic cranial skeleton morphogenesis / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / 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 / telomerase RNA binding / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / U4 snRNP / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / U1 snRNP / 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 / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / nuclear androgen receptor binding / precatalytic spliceosome / Notch-HLH transcription pathway / protein kinase inhibitor activity / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / SMAD binding / regulation of alternative mRNA splicing, via spliceosome / mitotic G2 DNA damage checkpoint signaling / associative learning Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Zhang X / Zhan X / Yan C / Shi Y | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 226.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 65.1 KB 65.1 KB | Display Display | ![]() |
Images | ![]() | 89.7 KB | ||
Others | ![]() | 193.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 532.5 KB | Display | ![]() |
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Full document | ![]() | 532 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iczMC ![]() 9646C ![]() 9647C ![]() 6id0C ![]() 6id1C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The 3.0 angstrom map of the human P 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 4.7 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 |
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143320 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |