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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11693 | |||||||||
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Title | Human pre-Bact-2 spliceosome core structure | |||||||||
![]() | Masked/sharpened map of the pre-Bact-2 spliceosome core structure. | |||||||||
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Function / homology | ![]() microfibril / regulation of retinoic acid receptor signaling pathway / regulation of vitamin D receptor signaling pathway / embryonic brain development / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / mRNA 3'-end processing / pre-mRNA binding / U2-type catalytic step 1 spliceosome ...microfibril / regulation of retinoic acid receptor signaling pathway / regulation of vitamin D receptor signaling pathway / embryonic brain development / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / mRNA 3'-end processing / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of protein targeting to mitochondrion / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / precatalytic spliceosome / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / SMAD binding / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / 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 / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / Cajal body / cellular response to retinoic acid / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / positive regulation of protein export from nucleus / nuclear receptor coactivator activity / response to cocaine / DNA damage checkpoint signaling / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / protein modification process / NOTCH1 Intracellular Domain Regulates Transcription / mRNA processing / fibrillar center / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / mRNA splicing, via spliceosome / positive regulation of protein import into nucleus / protein tag activity / transcription corepressor activity / calcium-dependent protein binding / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / nuclear membrane / transcription coactivator activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / cell cycle / intracellular membrane-bounded organelle / DNA repair / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / centrosome / chromatin / GTP binding / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Townsend C / Kastner B / Leelaram MN / 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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 34.1 KB 34.1 KB | Display Display | ![]() |
Images | ![]() | 33.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 220.1 KB | Display | ![]() |
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Full document | ![]() | 219.3 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7aavMC ![]() 7abfC ![]() 7abgC ![]() 7abhC ![]() 7abiC M: atomic model generated by this map C: citing same article ( |
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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
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Masked/sharpened map of the pre-Bact-2 spliceosome core structure. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : pre-Bact-2 spliceosomal core structure
+Supramolecule #1: pre-Bact-2 spliceosomal core structure
+Supramolecule #2: pre-Bact-2 spliceosomal core structure
+Supramolecule #3: MINX M3 pre-mRNA
+Macromolecule #1: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #2: Protein BUD31 homolog
+Macromolecule #3: Cell division cycle 5-like protein
+Macromolecule #4: Spliceosome-associated protein CWC15 homolog
+Macromolecule #5: Microfibrillar-associated protein 1
+Macromolecule #6: Pleiotropic regulator 1
+Macromolecule #8: Pre-mRNA-processing factor 17
+Macromolecule #9: Pre-mRNA-splicing factor 38A
+Macromolecule #10: Pre-mRNA-processing-splicing factor 8
+Macromolecule #11: Pre-mRNA-splicing factor RBM22
+Macromolecule #12: SNW domain-containing protein 1
+Macromolecule #13: Zinc finger matrin-type protein 2
+Macromolecule #17: Ubiquitin-like protein 5
+Macromolecule #7: MINX M3 pre-mRNA
+Macromolecule #14: U2 snRNA
+Macromolecule #15: U5 snRNA
+Macromolecule #16: U6 snRNA
+Macromolecule #18: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #19: MAGNESIUM ION
+Macromolecule #20: D-chiro inositol hexakisphosphate
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 1.0 sec. / Average electron dose: 2.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: cryoSPARC ab initio reconstruction |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 39336 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7aav: |