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Yorodumi- EMDB-30878: Focused refinement map of SF3B region of the activated human mino... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30878 | |||||||||
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Title | Focused refinement map of SF3B region of the activated human minor spliceosome | |||||||||
Map data | focused refinement of SF3B 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 / protein localization to microtubule / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / alternative mRNA splicing, via spliceosome ...regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein localization to microtubule / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / alternative mRNA splicing, via spliceosome / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / regulation of vitamin D receptor signaling pathway / 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 / 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 / 7-methylguanosine cap hypermethylation / Prp19 complex / snRNP binding / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / transcription regulator inhibitor activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / commitment complex / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / Notch binding / positive regulation of mRNA splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / U2 snRNP / Basigin interactions / RNA Polymerase II Transcription Termination / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / NOTCH3 Intracellular Domain Regulates Transcription / pattern recognition receptor activity / WD40-repeat domain binding / Cajal body / positive regulation of neurogenesis / U2-type prespliceosome / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of G1/S transition of mitotic cell cycle / precatalytic spliceosome / retinoic acid receptor signaling pathway / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / SMAD binding / regulation of RNA splicing / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNA binding / U5 snRNP / RHOBTB2 GTPase cycle / U2 snRNA binding / RNA processing / U6 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / pre-mRNA intronic binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 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_30878.map.gz | 770.9 MB | EMDB map data format | |
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Header (meta data) | emd-30878-v30.xml emd-30878.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_30878.png | 176.5 KB | ||
Others | emd_30878_additional_1.map.gz | 763.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30878 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30878 | HTTPS FTP |
-Validation report
Summary document | emd_30878_validation.pdf.gz | 330.6 KB | Display | EMDB validaton report |
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Full document | emd_30878_full_validation.pdf.gz | 330.1 KB | Display | |
Data in XML | emd_30878_validation.xml.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30878 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30878 | 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_30878.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | focused refinement of SF3B 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
-Additional map: focused refinement of SF3b130
File | emd_30878_additional_1.map | ||||||||||||
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Annotation | focused refinement of SF3b130 | ||||||||||||
Projections & Slices |
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Density Histograms |
-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 |
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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 / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4.0 nm / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 19.531 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101443 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |