+
Open data
-
Basic information
Entry | Database: PDB / ID: 7abf | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human pre-Bact-1 spliceosome core structure | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | SPLICING / Complex / spliceosome / catalytic activation | |||||||||||||||||||||
Function / homology | ![]() microfibril / regulation of retinoic acid receptor signaling pathway / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / transcription elongation factor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / positive regulation of mRNA splicing, via spliceosome / host-mediated activation of viral transcription / U2-type precatalytic spliceosome ...microfibril / regulation of retinoic acid receptor signaling pathway / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / transcription elongation factor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / positive regulation of mRNA splicing, via spliceosome / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / positive regulation of vitamin D receptor signaling pathway / mRNA cis splicing, via spliceosome / nuclear vitamin D receptor binding / RNA polymerase binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Notch binding / positive regulation of neurogenesis / RUNX3 regulates NOTCH signaling / U2-type catalytic step 2 spliceosome / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of protein targeting to mitochondrion / NOTCH3 Intracellular Domain Regulates Transcription / ubiquitin-like protein conjugating enzyme binding / WW domain binding / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / Notch-HLH transcription pathway / Formation of paraxial mesoderm / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / mRNA Splicing - Minor Pathway / negative regulation of transcription elongation by RNA polymerase II / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNP / protein localization to nucleus / positive regulation of G1/S transition of mitotic cell cycle / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / Cajal body / U1 snRNA binding / retinoic acid receptor signaling pathway / U4/U6 x U5 tri-snRNP complex / cellular response to retinoic acid / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / nuclear receptor binding / transcription coregulator activity / spliceosomal complex / response to cocaine / positive regulation of transcription elongation by RNA polymerase II / Downregulation of SMAD2/3:SMAD4 transcriptional activity / protein modification process / mRNA splicing, via spliceosome / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / protein tag activity / nuclear matrix / fibrillar center / mRNA processing / rRNA processing / transcription corepressor activity / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / single-stranded DNA binding / cellular response to lipopolysaccharide / microtubule cytoskeleton / nuclear membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / nuclear body / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / GTPase activity / centrosome / regulation of transcription by RNA polymerase II / chromatin / GTP binding / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() synthetic construct (others) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 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 | ![]() | 757.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 88.3 KB | Display | |
Data in CIF | ![]() | 145.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11694MC ![]() 7aavC ![]() 7abgC ![]() 7abhC ![]() 7abiC M: map data used to model this data C: citing same article ( |
---|---|
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
-Protein , 12 types, 12 molecules QIArNqRXvGKA4
#1: Protein | Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Protein | Mass: 37563.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 23664.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 8560.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 70098.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 61610.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 52050.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 121870.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 3 types, 3 molecules 56Z
#8: RNA chain | Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#9: RNA chain | Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: RNA chain | Mass: 73712.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules 




#16: Chemical | ChemComp-IHP / |
---|---|
#17: Chemical | ChemComp-GTP / |
#18: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
---|---|
Has protein modification | 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 | 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: ![]() |
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 |
-
Processing
EM software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84539 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |