+
Open data
-
Basic information
Entry | Database: PDB / ID: 7abi | ||||||
---|---|---|---|---|---|---|---|
Title | Human pre-Bact-2 spliceosome | ||||||
![]() |
| ||||||
![]() | SPLICING / Complex / spliceosome / catalytic activation | ||||||
Function / homology | ![]() RES complex / microfibril / somatic diversification of immunoglobulins / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding ...RES complex / microfibril / somatic diversification of immunoglobulins / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / 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 / embryonic brain development / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / miRNA processing / methylosome / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / 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 / transcription regulator inhibitor activity / 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 / SAGA complex / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / RHOBTB1 GTPase cycle / positive regulation of transcription by RNA polymerase III / Basigin interactions / U1 snRNP / positive regulation of protein targeting to mitochondrion / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / nuclear androgen receptor binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / 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 alternative mRNA splicing, via spliceosome / regulation of RNA splicing / blastocyst development / mRNA 3'-splice site recognition / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / localization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å | ||||||
![]() | Townsend, C. / Kastner, B. / Leelaram, M.N. / Bertram, K. / Stark, H. / Luehrmann, R. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 303.1 KB | Display | |
Data in CIF | ![]() | 532.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11697MC ![]() 7aavC ![]() 7abfC ![]() 7abgC ![]() 7abhC C: citing same article ( M: map data used to model this data |
---|---|
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]) |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules Ds
#1: Protein | Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#13: Protein | Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Splicing factor 3B subunit ... , 6 types, 6 molecules EwxzuT
#2: Protein | Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#5: Protein | Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#48: Protein | Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules bidkhalejcng
#3: Protein | Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #32: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #37: Protein | Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #40: Protein | Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #42: Protein | Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules WB
#4: Protein | Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#10: Protein | Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+Protein , 23 types, 24 molecules Uqv30Q1LNSrRY7KOyGotmfA8
-RNA chain , 4 types, 4 molecules 62Z5
#9: RNA chain | Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: accession number: NR_004394.1 / Source: (natural) ![]() |
---|---|
#30: RNA chain | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: accession number: NR_002716.3 / Source: (natural) ![]() |
#36: RNA chain | Mass: 103963.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#44: RNA chain | Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: accession number: X01691.1 / Source: (natural) ![]() |
-Pre-mRNA-splicing factor ... , 3 types, 3 molecules MIP
#26: Protein | Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#41: Protein | Mass: 37563.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Splicing factor 3A subunit ... , 3 types, 3 molecules pF4
#45: Protein | Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#46: Protein | Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#47: Protein | Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 3 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/IHP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/IHP.gif)
#50: Chemical | ChemComp-GTP / |
---|---|
#51: Chemical | ChemComp-MG / |
#52: Chemical | ChemComp-IHP / |
-Details
Has ligand of interest | N |
---|
-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) |
| ||||||||||||||||||||||||
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 | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 1 sec. / Electron dose: 2.27 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-
Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39336 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |