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Open data
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Basic information
Entry | Database: PDB / ID: 7abh | ||||||
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Title | Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion) | ||||||
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![]() | SPLICING / Complex / spliceosome / catalytic activation | ||||||
Function / homology | ![]() U11/U12 snRNP / B-WICH complex / miRNA processing / splicing factor binding / U12-type spliceosomal complex / Prp19 complex / mRNA 3'-end processing / blastocyst formation / RNA splicing, via transesterification reactions / regulation of mRNA splicing, via spliceosome ...U11/U12 snRNP / B-WICH complex / miRNA processing / splicing factor binding / U12-type spliceosomal complex / Prp19 complex / mRNA 3'-end processing / blastocyst formation / RNA splicing, via transesterification reactions / regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type spliceosomal complex / transcription regulator inhibitor activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / positive regulation of mRNA splicing, via spliceosome / RHOBTB1 GTPase cycle / U2 snRNP / RNA Polymerase II Transcription Termination / SAGA complex / positive regulation of transcription by RNA polymerase III / WD40-repeat domain binding / U2-type prespliceosome / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / RHOBTB2 GTPase cycle / U2 snRNA binding / Protein methylation / regulation of DNA repair / negative regulation of canonical NF-kappaB signal transduction / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / DNA damage checkpoint signaling / negative regulation of protein catabolic process / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / B-WICH complex positively regulates rRNA expression / positive regulation of neuron projection development / nuclear matrix / mRNA splicing, via spliceosome / mRNA processing / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / DNA replication / DNA recombination / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / nuclear speck / DNA repair / intracellular membrane-bounded organelle / mRNA binding / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 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
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 611.5 KB | Display | ![]() |
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PDB format | ![]() | 374.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11696MC ![]() 7aavC ![]() 7abfC ![]() 7abgC ![]() 7abiC 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
-Protein , 6 types, 6 molecules Ly01Y7
#1: Protein | Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 45880.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 37425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 102600.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#16: Protein | Mass: 45453.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 2 types, 2 molecules Z2
#3: RNA chain | Mass: 73712.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#15: RNA chain | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Splicing factor 3A subunit ... , 2 types, 2 molecules F4
#4: Protein | Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#5: Protein | Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Splicing factor 3B subunit ... , 6 types, 6 molecules uTEwxz
#6: Protein | Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#7: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: 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) ![]() |
-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 | Instrument: FEI VITROBOT MARK IV / 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: 2.25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39336 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |