+Open data
-Basic information
Entry | Database: PDB / ID: 7abg | ||||||
---|---|---|---|---|---|---|---|
Title | Human pre-Bact-1 spliceosome | ||||||
Components |
| ||||||
Keywords | SPLICING / Complex / spliceosome / catalytic activation | ||||||
Function / homology | Function and homology information snRNA export from nucleus / DNA topoisomerase binding / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / microfibril / positive regulation of mRNA 3'-end processing / Lsm2-8 complex / U6 snRNA 3'-end binding ...snRNA export from nucleus / DNA topoisomerase binding / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / microfibril / positive regulation of mRNA 3'-end processing / Lsm2-8 complex / U6 snRNA 3'-end binding / positive regulation of RNA export from nucleus / cap-dependent translational initiation / protein kinase B binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U11/U12 snRNP / U6 snRNP / Processing of Intronless Pre-mRNAs / regulation of retinoic acid receptor signaling pathway / PH domain binding / snRNP binding / snRNA binding / U2 snRNP binding / positive regulation of RNA binding / U7 snRNA binding / histone pre-mRNA DCP binding / RNA cap binding / U7 snRNP / WW domain binding / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / : / mRNA splice site recognition / miRNA processing / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / transcription elongation factor activity / protein methylation / RNA 7-methylguanosine cap binding / U12-type spliceosomal complex / methylosome / mRNA 3'-end processing / Transport of the SLBP independent Mature mRNA / P-body assembly / Transport of the SLBP Dependant Mature mRNA / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / blastocyst formation / pre-mRNA binding / U2-type catalytic step 1 spliceosome / Transport of Mature mRNA Derived from an Intronless Transcript / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / telomerase RNA binding / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / commitment complex / RNA catabolic process / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / nuclear vitamin D receptor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / ubiquitin-like protein conjugating enzyme binding / Notch binding / RNA polymerase binding / U4 snRNP / regulation of translational initiation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / SAGA complex / RUNX3 regulates NOTCH signaling / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription 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
| ||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7abg.cif.gz | 2.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
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 |
---|
-Related structure data
Related structure data | 11695MC 7aavC 7abfC 7abhC 7abiC M: map data used to model this data C: citing same article (ref.) |
---|---|
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 |
|
---|---|
1 |
|
-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 |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
---|---|
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 |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |