+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30879 | |||||||||
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Title | focused refinement map for the RBM48/ARMC7 region | |||||||||
Map data | focused refinement map for the RBM48/ARMC7 region | |||||||||
Sample |
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Function / homology | Function and homology information regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / histone pre-mRNA DCP binding / regulation of retinoic acid receptor signaling pathway ...regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / histone pre-mRNA DCP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNP / protein localization to microtubule / B-WICH complex / histone pre-mRNA 3'end processing complex / alternative mRNA splicing, via spliceosome / 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) / splicing factor binding / methylosome / protein methylation / U12-type spliceosomal complex / miRNA processing / 7-methylguanosine cap hypermethylation / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / Prp19 complex / blastocyst formation / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA 3'-end processing / : / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / positive regulation by host of viral transcription / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / U2 snRNP / SAGA complex / Notch binding / nuclear vitamin D receptor binding / positive regulation of transcription by RNA polymerase III / RNA Polymerase II Transcription Termination / Basigin interactions / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U1 snRNP / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / U2-type prespliceosome / NOTCH4 Intracellular Domain Regulates Transcription / pattern recognition receptor activity / K63-linked polyubiquitin modification-dependent protein binding / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / precatalytic spliceosome / nuclear androgen receptor binding / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / regulation of RNA splicing / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / antiviral innate immune response / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNP / retinoic acid receptor signaling pathway / localization / regulation of DNA repair / Cajal body / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding / RNA processing / canonical NF-kappaB signal transduction Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.24 Å | |||||||||
Authors | Bai R / Wan R | |||||||||
Funding support | China, 1 items
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Citation | Journal: Science / Year: 2021 Title: Structure of the activated human minor spliceosome. Authors: Rui Bai / Ruixue Wan / Lin Wang / Kui Xu / Qiangfeng Zhang / Jianlin Lei / Yigong Shi / Abstract: The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo- ...The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. The 5' splice site and branch point sequence of the U12-type intron are recognized by the U6atac and U12 small nuclear RNAs (snRNAs), respectively. Five newly identified proteins stabilize the conformation of the catalytic center: The zinc finger protein SCNM1 functionally mimics the SF3a complex of the major spliceosome, the RBM48-ARMC7 complex binds the γ-monomethyl phosphate cap at the 5' end of U6atac snRNA, the U-box protein PPIL2 coordinates loop I of U5 snRNA and stabilizes U5 small nuclear ribonucleoprotein (snRNP), and CRIPT stabilizes U12 snRNP. Our study provides a framework for the mechanistic understanding of the function of the human minor spliceosome. | |||||||||
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_30879.map.gz | 755.4 MB | EMDB map data format | |
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Header (meta data) | emd-30879-v30.xml emd-30879.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
Images | emd_30879.png | 246.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30879 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30879 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30879.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | focused refinement map for the RBM48/ARMC7 region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0742 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 : Structure of the Activated Human Minor Spliceosome (Bact Complex)
Entire | Name: Structure of the Activated Human Minor Spliceosome (Bact Complex) |
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Components |
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-Supramolecule #1: Structure of the Activated Human Minor Spliceosome (Bact Complex)
Supramolecule | Name: Structure of the Activated Human Minor Spliceosome (Bact Complex) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#45 |
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Source (natural) | Organism: Homo sapiens (human) / Strain: HeLa S3 / Location in cell: Nucleus |
Molecular weight | Experimental: 1.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.9 |
Grid | Model: Quantifoil / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4.0 nm |
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 19.531 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66297 |