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Open data
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Basic information
Entry | Database: PDB / ID: 7abg | ||||||
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Title | Human pre-Bact-1 spliceosome | ||||||
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![]() | SPLICING / Complex / spliceosome / catalytic activation | ||||||
Function / homology | ![]() positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / DNA topoisomerase binding / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding ...positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / DNA topoisomerase binding / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / protein kinase B binding / cap-dependent translational initiation / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / Processing of Intronless Pre-mRNAs / U11/U12 snRNP / snRNA binding / PH domain binding / regulation of retinoic acid receptor signaling pathway / RNA cap binding / WW domain binding / 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 / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / 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 / mRNA splice site recognition / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / Transport of the SLBP independent Mature mRNA / splicing factor binding / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap 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 / transcription elongation factor activity / 7-methylguanosine cap hypermethylation / Prp19 complex / positive regulation of androgen receptor activity / Transport of Mature mRNA Derived from an Intronless Transcript / snRNP binding / U1 snRNP binding / mRNA 3'-end processing / P-body assembly / pICln-Sm protein complex / blastocyst formation / mRNA 3'-end processing / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / RNA catabolic process / 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / commitment complex / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / RNA polymerase binding / U2-type catalytic step 2 spliceosome / ubiquitin-like protein conjugating enzyme binding / Notch binding / positive regulation of mRNA splicing, via spliceosome / regulation of translational initiation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / U2 snRNP / FGFR2 alternative splicing / RNA Polymerase II Transcription Termination / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å | ||||||
![]() | Townsend, C. / Kastner, B. / Leelaram, M.N. / Bertram, K. / Stark, H. / Luehrmann, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Authors: Cole Townsend / Majety N Leelaram / Dmitry E Agafonov / Olexandr Dybkov / Cindy L Will / Karl Bertram / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / ![]() Abstract: Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway ...Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 2.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11695MC ![]() 7aavC ![]() 7abfC ![]() 7abhC ![]() 7abiC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Motion-corrected micrographs (without dose-weighting) of human pre-Bact spliceosome [micrographs - single frame] Data #2: Motion-corrected micrographs (with dose-weighting) of human pre-Bact spliceosome [micrographs - single frame]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Nuclear cap-binding protein subunit ... , 2 types, 2 molecules A5A1
+U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules A2V9CHJA3
+Splicing factor 3B subunit ... , 6 types, 6 molecules zuTEwx
+Splicing factor 3A subunit ... , 3 types, 3 molecules Fp4
+U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules Ds
+U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules WB
+Protein , 17 types, 18 molecules QLRKyGAA4v0NrYA6mfqX
+RNA chain , 4 types, 4 molecules 52Z6
+Pre-mRNA-splicing factor ... , 2 types, 2 molecules IP
+Small nuclear ribonucleoprotein ... , 6 types, 12 molecules haiblekdjcng
+Non-polymers , 4 types, 4 molecules ![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTG.gif)
+Details
-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 | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||
Source (recombinant) | Organism: synthetic construct (others) | ||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R3.5/1 | ||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 | Average exposure time: 1 sec. / Electron dose: 2.25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3D reconstruction | Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84539 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |