+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 microfibril / RES complex / somatic diversification of immunoglobulins / U11/U12 snRNP / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding ...microfibril / RES complex / somatic diversification of immunoglobulins / U11/U12 snRNP / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / U7 snRNP / B-WICH complex / generation of catalytic spliceosome for first transesterification step / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of vitamin D receptor signaling pathway / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / embryonic brain development / splicing factor binding / miRNA processing / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / U1 snRNP binding / pICln-Sm protein complex / Prp19 complex / RNA splicing, via transesterification reactions / blastocyst formation / poly(A) binding / positive regulation of androgen receptor activity / mRNA 3'-end processing / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / positive regulation by host of viral transcription / U4 snRNP / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / transcription regulator inhibitor activity / U2 snRNP / nuclear vitamin D receptor binding / SAGA complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA Polymerase II Transcription Termination / RUNX3 regulates NOTCH signaling / positive regulation of transcription by RNA polymerase III / Basigin interactions / U1 snRNP / RHOBTB1 GTPase cycle / NOTCH4 Intracellular Domain Regulates Transcription / U2-type prespliceosome / ubiquitin-ubiquitin ligase activity / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of protein targeting to mitochondrion / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / precatalytic spliceosome / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of RNA splicing / SMAD binding / mRNA 3'-splice site recognition / blastocyst development / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNA binding / U5 snRNP / retinoic acid receptor signaling pathway / positive regulation of viral genome replication 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: |