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Yorodumi- PDB-9fmd: Integrative model of the human post-catalytic spliceosome (P-complex) -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fmd | ||||||
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Title | Integrative model of the human post-catalytic spliceosome (P-complex) | ||||||
Components |
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Keywords | SPLICING / P-complex / spliceosome | ||||||
Function / homology | Function and homology information regulation of homologous chromosome segregation / endoplasmic reticulum membrane organization / 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 / post-spliceosomal complex / cellular response to selenite ion / negative regulation of nitric-oxide synthase activity / spliceosomal complex disassembly ...regulation of homologous chromosome segregation / endoplasmic reticulum membrane organization / 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 / post-spliceosomal complex / cellular response to selenite ion / negative regulation of nitric-oxide synthase activity / spliceosomal complex disassembly / exon-exon junction complex / selenocysteine insertion sequence binding / NOSIP mediated eNOS trafficking / pre-mRNA 3'-splice site binding / protein exit from endoplasmic reticulum / granulocyte differentiation / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of toll-like receptor signaling pathway / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / alternative mRNA splicing, via spliceosome / renal system process / 3'-5' RNA helicase activity / U2 snRNP binding / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of interleukin-8 production / U7 snRNA binding / negative regulation of excitatory postsynaptic potential / histone pre-mRNA DCP binding / negative regulation of catalytic activity / U7 snRNP / generation of catalytic spliceosome for first transesterification step / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of phosphorylation / regulation of vitamin D receptor signaling pathway / histone pre-mRNA 3'end processing complex / negative regulation of lipopolysaccharide-mediated signaling pathway / cis assembly of pre-catalytic spliceosome / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Deadenylation of mRNA / molecular sequestering activity / negative regulation of interferon-beta production / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / embryonic brain development / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / positive regulation of androgen receptor activity / Prp19 complex / U1 snRNP binding / snRNP binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / embryonic cranial skeleton morphogenesis / pICln-Sm protein complex / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / regulation of nitric oxide biosynthetic process / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / positive regulation of vitamin D receptor signaling pathway / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / Notch binding / positive regulation of alpha-beta T cell differentiation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / RUNX3 regulates NOTCH signaling / U2 snRNP / NOTCH4 Intracellular Domain Regulates Transcription / RNA Polymerase II Transcription Termination / exploration behavior / U1 snRNP / positive regulation of neurogenesis / ubiquitin-ubiquitin ligase activity / NOTCH3 Intracellular Domain Regulates Transcription / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / lipid biosynthetic process Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human adenovirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Rothe, P. / Plaschka, C. / Vorlaender, M.K. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nature / Year: 2024 Title: Mechanism for the initiation of spliceosome disassembly. Authors: Matthias K Vorländer / Patricia Rothe / Justus Kleifeld / Eric D Cormack / Lalitha Veleti / Daria Riabov-Bassat / Laura Fin / Alex W Phillips / Luisa Cochella / Clemens Plaschka / Abstract: Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on ...Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on spliceosome assembly and remodelling for catalysis, but the mechanism of disassembly remains unclear. Here we report cryo-electron microscopy structures of nematode and human terminal intron lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 therefore controls both the start and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of the initiation of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes. #1: Journal: Science / Year: 2019 Title: A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation. Authors: Sebastian M Fica / Chris Oubridge / Max E Wilkinson / Andrew J Newman / Kiyoshi Nagai / Abstract: During exon ligation, the spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a ...During exon ligation, the spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo-electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3'SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5'-exon and intron 3'SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP-factors implicated in alternative splicing-further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3'SS selection and to potentially fine-tune alternative splicing at the exon ligation stage. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fmd.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9fmd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9fmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fmd_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 9fmd_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 9fmd_validation.xml.gz | 367.3 KB | Display | |
Data in CIF | 9fmd_validation.cif.gz | 620.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/9fmd ftp://data.pdbj.org/pub/pdb/validation_reports/fm/9fmd | HTTPS FTP |
-Related structure data
Related structure data | 4525M 8ro0C 8ro1C 8ro2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 24 types, 25 molecules 1325056789ACJLNNOPQRSRTVXZbiwz
+RNA chain , 4 types, 4 molecules 25EXIN
+Splicing factor ... , 3 types, 3 molecules 3Fx
+DNA chain , 1 types, 1 molecules 6
+U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules BE
+Pre-mRNA-splicing factor ... , 7 types, 7 molecules DHIKMOU
+Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Sy
+Pre-mRNA-processing factor ... , 2 types, 5 molecules Wqrst
+Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkelfmgn
+U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op
+Non-polymers , 6 types, 16 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103860 / Symmetry type: POINT |