+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11697 | |||||||||
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Title | Human pre-Bact-2 spliceosome | |||||||||
Map data | Unmasked/unsharpened map of the human pre-Bact-2 spliceosome. | |||||||||
Sample |
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Function / homology | Function and homology information RES complex / microfibril / somatic diversification of immunoglobulins / post-mRNA release spliceosomal complex / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / snRNP binding / U2 snRNP binding / U7 snRNA binding ...RES complex / microfibril / somatic diversification of immunoglobulins / post-mRNA release spliceosomal complex / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / regulation of vitamin D receptor signaling pathway / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / embryonic brain development / miRNA processing / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / blastocyst formation / pre-mRNA binding / 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 / telomerase RNA binding / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / commitment complex / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / transcription regulator inhibitor activity / Notch binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / nuclear vitamin D receptor binding / U4 snRNP / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / SAGA complex / RUNX3 regulates NOTCH signaling / Basigin interactions / U2 snRNP / RNA Polymerase II Transcription Termination / RHOBTB1 GTPase cycle / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / positive regulation of protein targeting to mitochondrion / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / cyclosporin A binding / precatalytic spliceosome / spliceosomal complex assembly / Notch-HLH transcription pathway / positive regulation of transcription by RNA polymerase I / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / regulation of RNA splicing / blastocyst development / mRNA 3'-splice site recognition / protein localization to nucleus / transcription-coupled nucleotide-excision repair / 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 / Protein methylation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 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_11697.map.gz | 171.3 MB | EMDB map data format | |
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Header (meta data) | emd-11697-v30.xml emd-11697.xml | 80.2 KB 80.2 KB | Display Display | EMDB header |
Images | emd_11697.png | 39.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11697 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11697 | HTTPS FTP |
-Related structure data
Related structure data | 7abiMC 7aavC 7abfC 7abgC 7abhC 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_11697.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 human 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
+Supramolecule #1: Human pre-Bact-2 spliceosome
+Supramolecule #2: Human pre-Bact-2 spliceosome
+Supramolecule #3: MINX M3 pre-mRNA
+Macromolecule #1: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #2: Splicing factor 3B subunit 3
+Macromolecule #3: Small nuclear ribonucleoprotein F
+Macromolecule #4: U2 small nuclear ribonucleoprotein A'
+Macromolecule #5: Splicing factor 3B subunit 4
+Macromolecule #6: Small nuclear ribonucleoprotein G
+Macromolecule #7: Intron-binding protein aquarius
+Macromolecule #8: Splicing factor 3B subunit 5
+Macromolecule #10: U2 small nuclear ribonucleoprotein B''
+Macromolecule #11: Splicing factor 3B subunit 6
+Macromolecule #12: Ubiquitin-like protein 5
+Macromolecule #13: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #14: SNW domain-containing protein 1
+Macromolecule #15: BUD13 homolog
+Macromolecule #16: Smad nuclear-interacting protein 1
+Macromolecule #17: Protein BUD31 homolog
+Macromolecule #18: RNA-binding motif protein, X-linked 2
+Macromolecule #19: Cell division cycle 5-like protein
+Macromolecule #20: Zinc finger matrin-type protein 2
+Macromolecule #21: Beta-catenin-like protein 1
+Macromolecule #22: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #23: Spliceosome-associated protein CWC15 homolog
+Macromolecule #24: Serine/arginine repetitive matrix protein 1
+Macromolecule #25: DNA/RNA-binding protein KIN17
+Macromolecule #26: Pre-mRNA-splicing factor SYF1
+Macromolecule #27: Microfibrillar-associated protein 1
+Macromolecule #28: Crooked neck-like protein 1
+Macromolecule #29: PHD finger-like domain-containing protein 5A
+Macromolecule #31: Pleiotropic regulator 1
+Macromolecule #32: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #33: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #34: RING-type E3 ubiquitin-protein ligase PPIL2
+Macromolecule #35: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #37: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #38: Pre-mRNA-processing-splicing factor 8
+Macromolecule #39: Pre-mRNA-processing factor 17
+Macromolecule #40: Small nuclear ribonucleoprotein E
+Macromolecule #41: Pre-mRNA-splicing factor 38A
+Macromolecule #42: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #43: Pre-mRNA-splicing factor RBM22
+Macromolecule #45: Splicing factor 3A subunit 1
+Macromolecule #46: Splicing factor 3A subunit 2
+Macromolecule #47: Splicing factor 3A subunit 3
+Macromolecule #48: Splicing factor 3B subunit 1
+Macromolecule #49: Splicing factor 3B subunit 2
+Macromolecule #9: U6 snRNA
+Macromolecule #30: U2 snRNA
+Macromolecule #36: MINX M3 pre-mRNA
+Macromolecule #44: U5 snRNA
+Macromolecule #50: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #51: MAGNESIUM ION
+Macromolecule #52: INOSITOL HEXAKISPHOSPHATE
-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 |
Vitrification | Cryogen name: ETHANE |
-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 / Average exposure time: 1.0 sec. / Average electron dose: 2.27 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: cryoSPARC ab initio |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.0 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-7abi: |