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Yorodumi- EMDB-30875: Cryo-EM Structure of the Activated Human Minor Spliceosome (minor... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30875 | |||||||||
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Title | Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex) | |||||||||
Map data | overall map of the activated human minor spliceosome | |||||||||
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 / regulation of postsynaptic density assembly / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / U2 snRNP binding ...regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein localization to microtubule / regulation of postsynaptic density assembly / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / 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 / protein methylation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / Prp19 complex / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / blastocyst formation / sno(s)RNA-containing ribonucleoprotein complex / snRNP binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / positive regulation by host of viral transcription / mRNA cis splicing, via spliceosome / positive regulation of vitamin D receptor signaling pathway / transcription regulator inhibitor activity / commitment complex / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type catalytic step 2 spliceosome / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / RUNX3 regulates NOTCH signaling / U2 snRNP / Basigin interactions / RHOBTB1 GTPase cycle / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / pattern recognition receptor activity / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / positive regulation of neurogenesis / U2-type prespliceosome / nuclear androgen receptor binding / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / 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 / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / SMAD binding / regulation of RNA splicing / protein localization to nucleus / postsynaptic density, intracellular component / 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 / positive regulation of G1/S transition of mitotic cell cycle / retinoic acid receptor signaling pathway / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / Cajal body Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Authors | Bai R / Wan R / Wang L / Xu K / Zhang Q / Lei J / Shi Y | |||||||||
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_30875.map.gz | 768.3 MB | EMDB map data format | |
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Header (meta data) | emd-30875-v30.xml emd-30875.xml | 65.5 KB 65.5 KB | Display Display | EMDB header |
Images | emd_30875.png | 240.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30875 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30875 | HTTPS FTP |
-Validation report
Summary document | emd_30875_validation.pdf.gz | 537.3 KB | Display | EMDB validaton report |
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Full document | emd_30875_full_validation.pdf.gz | 536.9 KB | Display | |
Data in XML | emd_30875_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | emd_30875_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30875 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30875 | HTTPS FTP |
-Related structure data
Related structure data | 7dvqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_30875.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | overall map of the activated human minor spliceosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : the activated human minor spliceosome (human minor Bact complex)
+Supramolecule #1: the activated human minor spliceosome (human minor Bact complex)
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #3: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #4: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #5: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #6: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #7: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #8: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #9: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #10: Small nuclear ribonucleoprotein F
+Macromolecule #11: Small nuclear ribonucleoprotein E
+Macromolecule #12: Small nuclear ribonucleoprotein G
+Macromolecule #16: Sodium channel modifier 1
+Macromolecule #17: Splicing factor 3B subunit 1
+Macromolecule #18: Splicing factor 3B subunit 2
+Macromolecule #19: Splicing factor 3B subunit 3
+Macromolecule #20: Splicing factor 3B subunit 4
+Macromolecule #21: Splicing factor 3B subunit 6
+Macromolecule #22: PHD finger-like domain-containing protein 5A
+Macromolecule #23: Splicing factor 3B subunit 5
+Macromolecule #24: Cell division cycle 5-like protein
+Macromolecule #25: Crooked neck-like protein 1
+Macromolecule #26: Spliceosome-associated protein CWC15 homolog
+Macromolecule #27: SNW domain-containing protein 1
+Macromolecule #28: Pleiotropic regulator 1
+Macromolecule #29: Smad nuclear-interacting protein 1
+Macromolecule #30: RNA-binding motif protein, X-linked 2
+Macromolecule #31: BUD13 homolog
+Macromolecule #32: RING-type E3 ubiquitin-protein ligase PPIL2
+Macromolecule #33: Peptidyl-prolyl cis-trans isomerase CWC27 homolog
+Macromolecule #34: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
+Macromolecule #35: G-patch domain and KOW motifs-containing protein
+Macromolecule #36: RING finger protein 113A
+Macromolecule #37: Serine/arginine repetitive matrix protein 2
+Macromolecule #38: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #39: Serine/arginine repetitive matrix protein 1
+Macromolecule #40: Cysteine-rich PDZ-binding protein
+Macromolecule #41: RNA-binding protein 48
+Macromolecule #42: Armadillo repeat-containing protein 7
+Macromolecule #2: U5 snRNA
+Macromolecule #13: U6atac snRNA
+Macromolecule #14: pre-mRNA
+Macromolecule #15: U12 snRNA
+Macromolecule #43: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #44: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #45: MAGNESIUM ION
+Macromolecule #46: POTASSIUM ION
+Macromolecule #47: 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]ox...
+Macromolecule #48: ZINC ION
+Macromolecule #49: water
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.89 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 |