+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11695 | |||||||||
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Title | Human pre-Bact-1 spliceosome | |||||||||
Map data | Unmasked/unsharpened map of the pre-Bact-1 complex. | |||||||||
Sample |
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Keywords | Complex / spliceosome / catalytic activation / splicing | |||||||||
Function / homology | Function and homology information snRNA export from nucleus / DNA topoisomerase binding / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / microfibril / positive regulation of mRNA 3'-end processing / Lsm2-8 complex / U6 snRNA 3'-end binding ...snRNA export from nucleus / DNA topoisomerase binding / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / microfibril / positive regulation of mRNA 3'-end processing / Lsm2-8 complex / U6 snRNA 3'-end binding / positive regulation of RNA export from nucleus / cap-dependent translational initiation / protein kinase B binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U11/U12 snRNP / U6 snRNP / Processing of Intronless Pre-mRNAs / regulation of retinoic acid receptor signaling pathway / PH domain binding / snRNP binding / snRNA binding / U2 snRNP binding / positive regulation of RNA binding / U7 snRNA binding / histone pre-mRNA DCP binding / RNA cap binding / U7 snRNP / WW domain binding / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / miRNA processing / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / transcription elongation factor activity / protein methylation / RNA 7-methylguanosine cap binding / U12-type spliceosomal complex / methylosome / mRNA 3'-end processing / nuclear retinoic acid receptor binding / Transport of the SLBP independent Mature mRNA / P-body assembly / Transport of the SLBP Dependant Mature mRNA / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / blastocyst formation / pre-mRNA binding / Transport of Mature mRNA Derived from an Intronless Transcript / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / regulation of mRNA splicing, via spliceosome / : / spliceosomal tri-snRNP complex / positive regulation of mRNA splicing, via spliceosome / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / RNA catabolic process / commitment complex / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / nuclear vitamin D receptor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / U4 snRNP / regulation of translational initiation / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / SAGA complex / RUNX3 regulates NOTCH signaling / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / nuclear-transcribed mRNA catabolic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
Authors | Townsend C / Kastner B | |||||||||
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_11695.map.gz | 170.7 MB | EMDB map data format | |
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Header (meta data) | emd-11695-v30.xml emd-11695.xml | 83.8 KB 83.8 KB | Display Display | EMDB header |
Images | emd_11695.png | 41.1 KB | ||
Filedesc metadata | emd-11695.cif.gz | 22 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11695 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11695 | HTTPS FTP |
-Related structure data
Related structure data | 7abgMC 7aavC 7abfC 7abhC 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_11695.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unmasked/unsharpened map of the pre-Bact-1 complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : pre-Bact-1 spliceosomal complex
+Supramolecule #1: pre-Bact-1 spliceosomal complex
+Supramolecule #2: pre-Bact-1 spliceosomal complex
+Macromolecule #1: Nuclear cap-binding protein subunit 1
+Macromolecule #2: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #3: Splicing factor 3B subunit 6
+Macromolecule #4: Splicing factor 3A subunit 2
+Macromolecule #5: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #6: U2 small nuclear ribonucleoprotein A'
+Macromolecule #7: U2 small nuclear ribonucleoprotein B''
+Macromolecule #8: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #9: Protein BUD31 homolog
+Macromolecule #10: Nuclear cap-binding protein subunit 2
+Macromolecule #12: Cell division cycle 5-like protein
+Macromolecule #13: Spliceosome-associated protein CWC15 homolog
+Macromolecule #14: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #15: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #16: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #17: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #18: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #20: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #21: Microfibrillar-associated protein 1
+Macromolecule #22: PHD finger-like domain-containing protein 5A
+Macromolecule #23: Pleiotropic regulator 1
+Macromolecule #25: Pre-mRNA-processing-splicing factor 8
+Macromolecule #26: Pre-mRNA-splicing factor 38A
+Macromolecule #27: Pre-mRNA-splicing factor RBM22
+Macromolecule #28: Splicing factor 3A subunit 1
+Macromolecule #29: Splicing factor 3A subunit 3
+Macromolecule #30: Transcription elongation regulator 1
+Macromolecule #31: Splicing factor 3B subunit 1
+Macromolecule #32: Splicing factor 3B subunit 2
+Macromolecule #33: Splicing factor 3B subunit 3
+Macromolecule #34: Splicing factor 3B subunit 4
+Macromolecule #35: Splicing factor 3B subunit 5
+Macromolecule #36: SNW domain-containing protein 1
+Macromolecule #37: Smad nuclear-interacting protein 1
+Macromolecule #38: Zinc finger matrin-type protein 2
+Macromolecule #39: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #40: Serine/arginine repetitive matrix protein 1
+Macromolecule #42: Serine/arginine-rich splicing factor 1
+Macromolecule #43: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #44: Small nuclear ribonucleoprotein F
+Macromolecule #45: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #46: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #47: Small nuclear ribonucleoprotein G
+Macromolecule #48: Small nuclear ribonucleoprotein E
+Macromolecule #49: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #50: Ubiquitin-like protein 5
+Macromolecule #51: WW domain-binding protein 11
+Macromolecule #11: U5 snRNA
+Macromolecule #19: U2 snRNA
+Macromolecule #24: MINX M3 pre-mRNA
+Macromolecule #41: U6 snRNA
+Macromolecule #52: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #53: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #54: MAGNESIUM ION
+Macromolecule #55: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
-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: 7.8 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 |
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Output model | PDB-7abg: |