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- PDB-7dvq: Cryo-EM Structure of the Activated Human Minor Spliceosome (minor... -
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Basic information
Entry | Database: PDB / ID: 7dvq | ||||||
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Title | Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex) | ||||||
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![]() | SPLICING / spliceosome / minor spliceosome / Bact complex / human spliceosome / PPIL2 / SCNM1 / RBM48-ARMC7 complex / U12-type intron / U6atac snRNA | ||||||
Function / homology | ![]() regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein localization to microtubule / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / alternative mRNA splicing, via spliceosome ...regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein localization to microtubule / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / alternative mRNA splicing, via spliceosome / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / regulation of vitamin D receptor signaling pathway / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / miRNA processing / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / Prp19 complex / snRNP binding / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / transcription regulator inhibitor activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / commitment complex / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / Notch binding / positive regulation of mRNA splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / U2 snRNP / Basigin interactions / RNA Polymerase II Transcription Termination / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / NOTCH3 Intracellular Domain Regulates Transcription / pattern recognition receptor activity / WD40-repeat domain binding / positive regulation of neurogenesis / U2-type prespliceosome / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / 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 RNA splicing / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / U5 snRNP / positive regulation of G1/S transition of mitotic cell cycle / RHOBTB2 GTPase cycle / U2 snRNA binding / RNA processing / U6 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / Cajal body / pre-mRNA intronic binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||
![]() | Bai, R. / Wan, R. / Wang, L. / Xu, K. / Zhang, Q. / Lei, J. / Shi, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the activated human minor spliceosome. Authors: Rui Bai / Ruixue Wan / Lin Wang / Kui Xu / Qiangfeng Zhang / Jianlin Lei / Yigong Shi / ![]() Abstract: The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo- ...The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. The 5' splice site and branch point sequence of the U12-type intron are recognized by the U6atac and U12 small nuclear RNAs (snRNAs), respectively. Five newly identified proteins stabilize the conformation of the catalytic center: The zinc finger protein SCNM1 functionally mimics the SF3a complex of the major spliceosome, the RBM48-ARMC7 complex binds the γ-monomethyl phosphate cap at the 5' end of U6atac snRNA, the U-box protein PPIL2 coordinates loop I of U5 snRNA and stabilizes U5 small nuclear ribonucleoprotein (snRNP), and CRIPT stabilizes U12 snRNP. Our study provides a framework for the mechanistic understanding of the function of the human minor spliceosome. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
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PDB format | ![]() | 1.9 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30875MC 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 , 20 types, 21 molecules ACbiv6LJPRTXYZ9zyM0IK
#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) ![]() | ||||||||||||||||||||||||||||||||||
#7: Protein | Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein | | Mass: 25993.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #22: Protein | | Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #24: Protein | | Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #25: Protein | | Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #26: Protein | | Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #27: Protein | | Mass: 61610.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #28: Protein | | Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #29: Protein | | Mass: 45880.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #30: Protein | | Mass: 37425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #31: Protein | | Mass: 70669.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #32: Protein | | Mass: 58910.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q13356, RING-type E3 ubiquitin transferase #33: Protein | | Mass: 53941.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #35: Protein | | Mass: 52299.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #36: Protein | | Mass: 38847.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #40: Protein | | Mass: 11239.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #41: Protein | | Mass: 41878.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #42: Protein | | Mass: 21946.039 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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#13: RNA chain | Mass: 39876.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: RNA chain | Mass: 44322.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#15: RNA chain | Mass: 48353.625 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) ![]() |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkfmelgn
#6: Protein | Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Splicing factor 3B subunit ... , 6 types, 6 molecules 123457
#17: Protein | Mass: 146104.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#18: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#19: Protein | Mass: 135798.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#20: Protein | Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: Protein | Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#23: Protein | Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Pre-mRNA-splicing factor ... , 2 types, 2 molecules xV
#34: Protein | Mass: 119443.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#38: Protein | Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Serine/arginine repetitive matrix protein ... , 2 types, 2 molecules U8
#37: Protein | Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#39: Protein | Mass: 102600.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 7 types, 20 molecules ![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/G5J.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/G5J.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#43: Chemical | ChemComp-IHP / | ||||||||
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#44: Chemical | ChemComp-GTP / | ||||||||
#45: Chemical | ChemComp-MG / #46: Chemical | #47: Chemical | ChemComp-G5J / | #48: Chemical | ChemComp-ZN / #49: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: the activated human minor spliceosome (human minor Bact complex) Type: COMPLEX / Entity ID: #1-#12, #14-#42 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.9 |
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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101443 / Symmetry type: POINT |