+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11694 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human pre-Bact-1 spliceosome core structure | |||||||||
Map data | Sharpened/masked map for pre-Bact-1 core structure. | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information microfibril / regulation of retinoic acid receptor signaling pathway / WW domain binding / regulation of vitamin D receptor signaling pathway / transcription elongation factor activity / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions ...microfibril / regulation of retinoic acid receptor signaling pathway / WW domain binding / regulation of vitamin D receptor signaling pathway / transcription elongation factor activity / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / positive regulation of mRNA splicing, via spliceosome / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / positive regulation of vitamin D receptor signaling pathway / Notch binding / U2-type catalytic step 2 spliceosome / nuclear vitamin D receptor binding / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of protein targeting to mitochondrion / 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 / Formation of paraxial mesoderm / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Minor Pathway / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / positive regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / U5 snRNP / U2 snRNA binding / Cajal body / U6 snRNA binding / pre-mRNA intronic binding / cellular response to retinoic acid / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / nuclear receptor coactivator activity / RNA splicing / response to cocaine / nuclear receptor binding / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / Downregulation of SMAD2/3:SMAD4 transcriptional activity / spliceosomal complex / protein modification process / NOTCH1 Intracellular Domain Regulates Transcription / protein tag activity / fibrillar center / mRNA processing / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / rRNA processing / Pre-NOTCH Transcription and Translation / mRNA splicing, via spliceosome / nuclear matrix / transcription corepressor activity / cellular response to xenobiotic stimulus / single-stranded DNA binding / cellular response to tumor necrosis factor / nuclear membrane / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear body / nuclear speck / intracellular membrane-bounded organelle / GTPase activity / centrosome / negative regulation of DNA-templated transcription / chromatin / GTP binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Townsend C / Kastner B / Leelaram MN / Bertram K / Stark H / Luehrmann R | |||||||||
Funding support | Germany, 1 items
| |||||||||
Citation | Journal: Science / Year: 2020 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 |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11694.map.gz | 14.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11694-v30.xml emd-11694.xml | 32.5 KB 32.5 KB | Display Display | EMDB header |
Images | emd_11694.png | 33.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11694 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11694 | HTTPS FTP |
-Related structure data
Related structure data | 7abfMC 7aavC 7abgC 7abhC 7abiC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10616 (Title: Cryo-EM dataset of human pre-Bact spliceosome / Data size: 584.5 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 | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11694.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened/masked map for pre-Bact-1 core structure. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : pre-Bact-1 spliceosomal complex
+Supramolecule #1: pre-Bact-1 spliceosomal complex
+Supramolecule #2: pre-Bact-1 spliceosomal complex
+Supramolecule #3: MINX M3 RNA
+Macromolecule #1: Protein BUD31 homolog
+Macromolecule #2: Pre-mRNA-splicing factor 38A
+Macromolecule #3: Pre-mRNA-processing-splicing factor 8
+Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #5: Zinc finger matrin-type protein 2
+Macromolecule #6: Ubiquitin-like protein 5
+Macromolecule #7: Spliceosome-associated protein CWC15 homolog
+Macromolecule #10: WW domain-binding protein 11
+Macromolecule #11: SNW domain-containing protein 1
+Macromolecule #12: Pleiotropic regulator 1
+Macromolecule #14: Microfibrillar-associated protein 1
+Macromolecule #15: Transcription elongation regulator 1
+Macromolecule #8: U5 small nuclear RNA
+Macromolecule #9: U6 small nuclear RNA
+Macromolecule #13: MINX M3 RNA
+Macromolecule #16: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #17: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #18: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | 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 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: cryoSPARC ab initio reconstruction |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 84539 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|---|
Output model | PDB-7abf: |