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- PDB-5xjc: Cryo-EM structure of the human spliceosome just prior to exon lig... -
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Basic information
Entry | Database: PDB / ID: 5xjc | |||||||||
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Title | Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom | |||||||||
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![]() | SPLICING / RNA splicing / human spliceosome / C* complex / atomic structure / step 2 factors / EJC | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Zhang, X. / Yan, C. / Hang, J. / Finci, I.L. / Lei, J. / Shi, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An Atomic Structure of the Human Spliceosome. Authors: Xiaofeng Zhang / Chuangye Yan / Jing Hang / Lorenzo I Finci / Jianlin Lei / Yigong Shi / ![]() Abstract: Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the ...Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the human spliceosome just before exon ligation (the C complex) at an average resolution of 3.76 Å. The splicing factor Prp17 stabilizes the active site conformation. The step II factor Slu7 adopts an extended conformation, binds Prp8 and Cwc22, and is poised for selection of the 3'-splice site. Remarkably, the intron lariat traverses through a positively charged central channel of RBM22; this unusual organization suggests mechanisms of intron recruitment, confinement, and release. The protein PRKRIP1 forms a 100-Å α helix linking the distant U2 snRNP to the catalytic center. A 35-residue fragment of the ATPase/helicase Prp22 latches onto Prp8, and the quaternary exon junction complex (EJC) recognizes upstream 5'-exon sequences and associates with Cwc22 and the GTPase Snu114. These structural features reveal important mechanistic insights into exon ligation. | |||||||||
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 | ![]() | 3.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 392.4 KB | Display | |
Data in CIF | ![]() | 618.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6721MC 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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Components
-Protein , 18 types, 19 molecules ACJLNPQRSTUXYbiuvwx
#1: Protein | Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
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#3: Protein | Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#10: Protein | Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#12: Protein | Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#14: Protein | Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#16: Protein | Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#17: Protein | Mass: 171502.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#18: Protein | Mass: 61770.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#19: Protein | Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#20: Protein | Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#21: Protein | Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#24: Protein | Mass: 21040.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#25: Protein | Mass: 139508.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
#28: Protein | Mass: 23686.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #37: Protein | | Mass: 46930.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #38: Protein | | Mass: 17301.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #39: Protein | | Mass: 19925.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #40: Protein | | Mass: 76381.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 4 types, 4 molecules BFGH
#2: RNA chain | Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#6: RNA chain | Mass: 34404.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: RNA chain | Mass: 87977.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#8: RNA chain | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules DE
#4: Protein | Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#5: Protein | Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Pre-mRNA-splicing factor ... , 6 types, 6 molecules IKMOVZ
#9: Protein | Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#11: Protein | Mass: 26163.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 28780.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#22: Protein | Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 68510.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Pre-mRNA-processing factor ... , 2 types, 5 molecules Wqrst
#23: Protein | Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#36: 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 |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkfmelgn
#27: Protein | Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #29: Protein | Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #30: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #31: Protein | Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #32: Protein | Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #33: Protein | Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op
#34: Protein | Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#35: Protein | Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 6 types, 24 molecules ![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ATP.gif)
#41: Chemical | ChemComp-IHP / | ||||||
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#42: Chemical | ChemComp-GTP / | ||||||
#43: Chemical | ChemComp-MG / #44: Chemical | #45: Chemical | ChemComp-ZN / #46: Chemical | |
-Details
Sequence details | The UNK reisue between G-1 and G1 is added intentionally as per authors request to fill in the ...The UNK reisue between G-1 and G1 is added intentionally as per authors request to fill in the cleavage by RNA splicing. |
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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
Component | Name: human C* spliceosome / Type: COMPLEX / Entity ID: #1-#40 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: 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 / Cs: 2.7 mm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Average exposure time: 0.25 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 5 / Num. of real images: 7308 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter upper: 10 eV / Energyfilter lower: 0 eV / Chromatic aberration corrector: -10 |
Image scans | Movie frames/image: 32 / Used frames/image: 2-32 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100085 / Symmetry type: POINT | ||||||||||||||||
Refinement | Highest resolution: 3.6 Å |