+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-11696 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion) | |||||||||
![]() | Masked/sharpened map of SF3b/U2 snRNP region of pre-Bact-2 spliceosome. | |||||||||
![]() |
| |||||||||
![]() | Complex / spliceosome / catalytic activation / splicing | |||||||||
Function / homology | ![]() U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / miRNA processing / 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 / splicing factor binding / U12-type spliceosomal complex / miRNA processing / Prp19 complex / mRNA 3'-end processing / blastocyst formation / RNA splicing, via transesterification reactions / regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / U2-type precatalytic spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U2 snRNP / SAGA complex / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / RHOBTB1 GTPase cycle / positive regulation of transcription by RNA polymerase III / WD40-repeat domain binding / U2-type prespliceosome / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / localization / RHOBTB2 GTPase cycle / Protein methylation / U2 snRNA binding / 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 / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA processing / nuclear matrix / positive regulation of neuron projection development / mRNA splicing, via spliceosome / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / DNA recombination / DNA replication / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / chromatin remodeling / cell cycle / intracellular membrane-bounded organelle / DNA repair / mRNA binding / DNA damage response / protein-containing complex binding / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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 | ![]()
| |||||||||
![]() | ![]() 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 | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 12.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 34 KB 34 KB | Display Display | ![]() |
Images | ![]() | 25 KB | ||
Filedesc metadata | ![]() | 11.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 349.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 349 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive 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 |
---|---|
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
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Masked/sharpened map of SF3b/U2 snRNP region of pre-Bact-2 spliceosome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
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 |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.9 |
---|---|
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 |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |
-
Image processing
Startup model | Type of model: OTHER / Details: cryoSPARC ab initio reconstruction |
---|---|
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 |
---|---|
Output model | ![]() PDB-7abh: |