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Open data
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Basic information
Entry | Database: PDB / ID: 7abi | |||||||||||||||
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Title | Human pre-Bact-2 spliceosome | |||||||||||||||
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![]() | SPLICING / Complex / spliceosome / catalytic activation | |||||||||||||||
Function / homology | ![]() microfibril / RES complex / somatic diversification of immunoglobulins / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity ...microfibril / RES complex / somatic diversification of immunoglobulins / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / U7 snRNP / generation of catalytic spliceosome for first transesterification step / histone pre-mRNA 3'end processing complex / 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 / B-WICH complex / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / miRNA processing / nuclear retinoic acid receptor binding / embryonic brain development / protein methylation / U12-type spliceosomal complex / poly(A) binding / 7-methylguanosine cap hypermethylation / RNA splicing, via transesterification reactions / U1 snRNP binding / mRNA 3'-end processing / sno(s)RNA-containing ribonucleoprotein complex / methylosome / blastocyst formation / regulation of mRNA splicing, via spliceosome / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / positive regulation of mRNA splicing, via spliceosome / snRNP binding / small nuclear ribonucleoprotein complex / splicing factor binding / SMN-Sm protein complex / P granule / host-mediated activation of viral transcription / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / telomerase RNA binding / U2-type spliceosomal complex / positive regulation of vitamin D receptor signaling pathway / telomerase holoenzyme complex / commitment complex / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / SAGA complex / U4 snRNP / RHOBTB1 GTPase cycle / U2 snRNP / RNA Polymerase II Transcription Termination / positive regulation of protein targeting to mitochondrion / U1 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / WD40-repeat domain binding / Basigin interactions / ubiquitin-ubiquitin ligase activity / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / cyclosporin A binding / Notch-HLH transcription pathway / Formation of paraxial mesoderm / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / regulation of RNA splicing / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / spliceosomal tri-snRNP complex assembly / Prp19 complex / blastocyst development / 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 / spliceosomal snRNP assembly 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 | ![]()
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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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Download
PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
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PDB format | ![]() | 1.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 301.3 KB | Display | |
Data in CIF | ![]() | 532.2 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 |
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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
-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) ![]() |
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#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) ![]() |
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#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) ![]() |
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-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) ![]() |
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#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) ![]() |
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#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) ![]() |
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#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) ![]() |
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#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 




#50: Chemical | ChemComp-GTP / |
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#51: Chemical | ChemComp-MG / |
#52: Chemical | ChemComp-IHP / |
-Details
Has ligand of interest | N |
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Has protein modification | N |
-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) |
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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 |
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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: 2.27 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software |
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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 |