+Open data
-Basic information
Entry | Database: PDB / ID: 7abg | ||||||
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Title | Human pre-Bact-1 spliceosome | ||||||
Components |
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Keywords | SPLICING / Complex / spliceosome / catalytic activation | ||||||
Function / homology | Function and homology information snRNA export from nucleus / DNA topoisomerase binding / nuclear cap binding complex / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing ...snRNA export from nucleus / DNA topoisomerase binding / nuclear cap binding complex / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / protein kinase B binding / U11/U12 snRNP / snRNP binding / U6 snRNP / PH domain binding / U2 snRNP binding / Processing of Intronless Pre-mRNAs / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / snRNA binding / positive regulation of RNA binding / B-WICH complex / RNA cap binding / histone pre-mRNA 3'end processing complex / WW domain binding / alternative mRNA splicing, via spliceosome / cis assembly of pre-catalytic spliceosome / regulation of vitamin D receptor signaling pathway / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / : / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / mRNA splice site recognition / splicing factor binding / miRNA processing / protein methylation / U12-type spliceosomal complex / methylosome / P-body assembly / transcription elongation factor activity / RNA 7-methylguanosine cap binding / mRNA 3'-end processing / 7-methylguanosine cap hypermethylation / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / U1 snRNP binding / pICln-Sm protein complex / Prp19 complex / RNA splicing, via transesterification reactions / blastocyst formation / positive regulation of androgen receptor activity / mRNA 3'-end processing / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / positive regulation by host of viral transcription / RNA catabolic process / U4 snRNP / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / transcription regulator inhibitor activity / U2 snRNP / nuclear vitamin D receptor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / ubiquitin-like protein conjugating enzyme binding / SAGA complex / RNA polymerase binding / regulation of translational initiation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process / RUNX3 regulates NOTCH signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å | ||||||
Authors | Townsend, C. / Kastner, B. / Leelaram, M.N. / Bertram, K. / Stark, H. / Luehrmann, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Science / Year: 2020 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7abg.cif.gz | 2.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7abg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7abg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/7abg ftp://data.pdbj.org/pub/pdb/validation_reports/ab/7abg | 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 (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10616 (Title: Cryo-EM dataset of human pre-Bact spliceosome / Data size: 584.5 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]) |
-Links
-Assembly
Deposited unit |
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1 |
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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
+Details
-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 | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||
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 |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
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 |
-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 |