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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11696 | |||||||||
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Title | Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion) | |||||||||
![]() | Masked/sharpened map of SF3b/U2 snRNP region of pre-Bact-2 spliceosome. | |||||||||
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![]() | Complex / spliceosome / catalytic activation / splicing | |||||||||
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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Townsend C / Kastner B | |||||||||
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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 34 KB 34 KB | Display Display | ![]() |
Images | ![]() | 25 KB | ||
Filedesc metadata | ![]() | 11.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7abhMC ![]() 7aavC ![]() 7abfC ![]() 7abgC ![]() 7abiC C: citing same article ( M: atomic model generated by this map |
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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 SF3b/U2 snRNP region of pre-Bact-2 spliceosome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion)
+Supramolecule #1: Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion)
+Supramolecule #2: Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion)
+Supramolecule #3: MINX M3 pre-mRNA
+Macromolecule #1: Cell division cycle 5-like protein
+Macromolecule #2: PHD finger-like domain-containing protein 5A
+Macromolecule #4: Splicing factor 3A subunit 2
+Macromolecule #5: Splicing factor 3A subunit 3
+Macromolecule #6: Splicing factor 3B subunit 1
+Macromolecule #7: Splicing factor 3B subunit 2
+Macromolecule #8: Splicing factor 3B subunit 3
+Macromolecule #9: Splicing factor 3B subunit 4
+Macromolecule #10: Splicing factor 3B subunit 5
+Macromolecule #11: Splicing factor 3B subunit 6
+Macromolecule #12: Smad nuclear-interacting protein 1
+Macromolecule #13: RNA-binding motif protein, X-linked 2
+Macromolecule #14: Serine/arginine repetitive matrix protein 1
+Macromolecule #16: DNA/RNA-binding protein KIN17
+Macromolecule #3: MINX M3 pre-mRNA
+Macromolecule #15: U2 snRNA
-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: 4.5 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-7abh: |