+Open data
-Basic information
Entry | Database: PDB / ID: 6qdv | |||||||||
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Title | Human post-catalytic P complex spliceosome | |||||||||
Components |
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Keywords | SPLICING / spliceosome / RNA / complex | |||||||||
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 / granulocyte differentiation / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / histone pre-mRNA DCP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNP / negative regulation of toll-like receptor signaling pathway / 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 / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / negative regulation of interleukin-8 production / regulation of mRNA processing / negative regulation of lipopolysaccharide-mediated signaling pathway / 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 / negative regulation of interferon-beta production / 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 / positive regulation of alpha-beta T cell differentiation / 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 / hematopoietic stem cell proliferation / nuclear androgen receptor binding / cyclosporin A binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Human adenovirus 2 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Fica, S.M. / Oubridge, C. / Wilkinson, M.E. / Newman, A.J. / Nagai, K. | |||||||||
Funding support | United Kingdom, 2items
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Citation | 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6qdv.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6qdv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6qdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/6qdv ftp://data.pdbj.org/pub/pdb/validation_reports/qd/6qdv | HTTPS FTP |
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-Related structure data
Related structure data | 4525MC 4526C 4527C 4528C 4529C 4530C 4532C 4533C 4534C 4535C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules 256EI
#1: RNA chain | Mass: 60459.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: RNA chain | Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36515 |
#3: RNA chain | Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#11: RNA chain | Mass: 4437.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 2 |
#15: RNA chain | Mass: 27772.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 2 |
-Protein , 18 types, 19 molecules 789ACDFGJKLOPSUVbki
#4: Protein | Mass: 44691.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P38919, RNA helicase | ||
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#5: Protein | Mass: 10370.526 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5S9 | ||
#6: Protein | Mass: 16929.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A72 | ||
#7: Protein | Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9 | ||
#9: Protein | Mass: 101231.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029 | ||
#10: Protein | Mass: 14476.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H875 | ||
#12: Protein | Mass: 15210.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUQ7 | ||
#13: Protein | Mass: 7269.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y421 | ||
#16: Protein | Mass: 35782.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660 | ||
#17: Protein | Mass: 33819.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573 | ||
#18: Protein | Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223 | ||
#21: Protein | Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459 | ||
#22: Protein | Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013 | ||
#24: Protein | Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0 | ||
#26: Protein | Mass: 171502.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60306, RNA helicase | ||
#27: Protein | Mass: 139522.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHX8, DDX8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q14562, RNA helicase | ||
#31: Protein | Mass: 9551.284 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678 #38: Protein | | Mass: 18055.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase |
-U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules BN
#8: Protein | Mass: 197053.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase |
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#20: Protein | Mass: 34092.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7 |
-Pre-mRNA-splicing factor ... , 6 types, 6 molecules HMTcsy
#14: Protein | Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8 |
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#19: Protein | Mass: 33156.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64 |
#25: Protein | Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7 |
#32: Protein | Mass: 68510.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95391 |
#41: Protein | Mass: 26163.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75934 |
#43: Protein | Mass: 17302.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95926 |
-Protein/peptide , 3 types, 3 molecules RZz
#23: Protein/peptide | Mass: 2767.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35 |
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#30: Protein/peptide | Mass: 3321.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N5F7 |
#44: Protein/peptide | Mass: 4036.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6IQ49 |
-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules WY
#28: Protein | Mass: 18697.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661 |
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#29: Protein | Mass: 10688.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579 |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules dnepfqgrhljm
#33: Protein | Mass: 9460.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318 #34: Protein | Mass: 9582.185 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304 #35: Protein | Mass: 8038.415 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306 #36: Protein | Mass: 8160.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308 #37: Protein | Mass: 9086.731 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314 #39: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316 |
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-Pre-mRNA-processing factor ... , 2 types, 5 molecules otuvw
#40: Protein | Mass: 59116.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508 |
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#42: Protein | Mass: 55245.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase |
-Non-polymers , 6 types, 18 molecules
#45: Chemical | ChemComp-MG / #46: Chemical | ChemComp-K / | #47: Chemical | ChemComp-ATP / | #48: Chemical | ChemComp-GTP / | #49: Chemical | ChemComp-ZN / #50: Chemical | ChemComp-IHP / | |
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-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 | Value: 3.0 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: 3 uL sample was applied to the grid, left for 25s, then blotted for 2.5-3.5s and immediately plunged into liquid 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 FIELDBright-field microscopy / Nominal magnification: 135000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 10 sec. / Electron dose: 53 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6200 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103860 / Symmetry type: POINT |