+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11696 | |||||||||
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Title | Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion) | |||||||||
Map data | Masked/sharpened map of SF3b/U2 snRNP region of pre-Bact-2 spliceosome. | |||||||||
Sample |
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Function / homology | Function and homology information U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / miRNA processing / RNA splicing, via transesterification reactions / Prp19 complex / blastocyst formation / mRNA 3'-end processing / : ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / miRNA processing / RNA splicing, via transesterification reactions / Prp19 complex / blastocyst formation / mRNA 3'-end processing / : / U2-type spliceosomal complex / positive regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2 snRNP / SAGA complex / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / RHOBTB1 GTPase cycle / U2-type prespliceosome / WD40-repeat domain binding / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / localization / regulation of DNA repair / canonical NF-kappaB signal transduction / Protein methylation / U2 snRNA binding / RHOBTB2 GTPase cycle / 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 / positive regulation of neuron projection development / mRNA splicing, via spliceosome / mRNA processing / nuclear matrix / 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 / DNA repair / mRNA binding / intracellular membrane-bounded organelle / 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 / membrane / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Townsend C / Kastner B / Leelaram MN / Bertram K / Stark H / Luehrmann R | |||||||||
Funding support | Germany, 1 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11696.map.gz | 12.2 MB | EMDB map data format | |
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Header (meta data) | emd-11696-v30.xml emd-11696.xml | 33.1 KB 33.1 KB | Display Display | EMDB header |
Images | emd_11696.png | 25 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11696 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11696 | HTTPS FTP |
-Related structure data
Related structure data | 7abhMC 7aavC 7abfC 7abgC 7abiC C: citing same article (ref.) M: atomic model generated by this map |
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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 |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11696.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
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 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7abh: |