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Open data
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Basic information
Entry | Database: PDB / ID: 6qdv | |||||||||
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Title | Human post-catalytic P complex spliceosome | |||||||||
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![]() | SPLICING / spliceosome / RNA / complex | |||||||||
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 / granulocyte differentiation / post-mRNA release spliceosomal complex ...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 / granulocyte differentiation / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / 3'-5' RNA helicase activity / U2 snRNP binding / negative regulation of toll-like receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / renal system process / generation of catalytic spliceosome for first transesterification step / 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 / Deadenylation of mRNA / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of interleukin-8 production / 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 / negative regulation of lipopolysaccharide-mediated signaling pathway / selenocysteine insertion sequence binding / embryonic brain development / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / poly(A) binding / U12-type spliceosomal complex / negative regulation of phosphorylation / methylosome / M-decay: degradation of maternal mRNAs by maternally stored factors / negative regulation of interferon-beta production / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / U1 snRNP binding / mRNA 3'-end processing / pICln-Sm protein complex / pre-mRNA binding / embryonic cranial skeleton morphogenesis / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / ATP-dependent activity, acting on RNA / small nuclear ribonucleoprotein complex / 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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RUNX3 regulates NOTCH signaling / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / positive regulation of alpha-beta T cell differentiation / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / U1 snRNP / 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 / hematopoietic stem cell proliferation / cyclosporin A binding / nuclear androgen receptor binding / negative regulation of type I interferon-mediated signaling pathway / snoRNA binding / negative regulation of NF-kappaB transcription factor activity / precatalytic spliceosome Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Fica, S.M. / Oubridge, C. / Wilkinson, M.E. / Newman, A.J. / Nagai, K. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.7 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 319 KB | Display | |
Data in CIF | ![]() | 540 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data |
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Links
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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) ![]() |
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#2: RNA chain | Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: RNA chain | Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: RNA chain | Mass: 4437.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#15: RNA chain | Mass: 27772.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-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) ![]() | ||
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#5: Protein | Mass: 10370.526 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#6: Protein | Mass: 16929.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#7: Protein | Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#9: Protein | Mass: 101231.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#10: Protein | Mass: 14476.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#12: Protein | Mass: 15210.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#13: Protein | Mass: 7269.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#16: Protein | Mass: 35782.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#17: Protein | Mass: 33819.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#18: Protein | Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#21: Protein | Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#22: Protein | Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#24: Protein | Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#26: Protein | Mass: 171502.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#27: Protein | Mass: 139522.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#31: Protein | Mass: 9551.284 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #38: Protein | | Mass: 18055.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#20: Protein | Mass: 34092.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#19: Protein | Mass: 33156.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#32: Protein | Mass: 68510.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 26163.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 17302.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#30: Protein/peptide | Mass: 3321.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#44: Protein/peptide | Mass: 4036.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#29: Protein | Mass: 10688.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() #34: Protein | Mass: 9582.185 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #35: Protein | Mass: 8038.415 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #36: Protein | Mass: 8160.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #37: Protein | Mass: 9086.731 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #39: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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) ![]() |
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#42: Protein | Mass: 55245.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase |
-Non-polymers , 6 types, 18 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/IHP.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/IHP.gif)
#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 |
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Sample preparation
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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. |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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 |
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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 |