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- EMDB-18225: cryo-EM structure of the human spliceosomal B complex protomer (t... -
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Open data
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Basic information
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Title | cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region) | |||||||||
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![]() | spliceosome / pre-catalytic spliceosome / spliceosomal B complex / SPLICING | |||||||||
Function / homology | ![]() microfibril / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component ...microfibril / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / box C/D methylation guide snoRNP complex / U4/U6 snRNP / transcription elongation factor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / U4 snRNA binding / snRNP binding / proline-rich region binding / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / RNA polymerase binding / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / U4 snRNP / U2 snRNP / positive regulation of protein targeting to mitochondrion / U3 snoRNA binding / ubiquitin-like protein conjugating enzyme binding / U2-type prespliceosome / rRNA modification in the nucleus and cytosol / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / negative regulation of transcription elongation by RNA polymerase II / MLL1 complex / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / single fertilization / U6 snRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / pre-mRNA intronic binding / spliceosomal snRNP assembly / RNA processing / ribonucleoprotein complex binding / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / nuclear receptor binding / maturation of SSU-rRNA / transcription coregulator activity / small-subunit processome / spliceosomal complex / positive regulation of transcription elongation by RNA polymerase II / response to cocaine / protein modification process / mRNA splicing, via spliceosome / protein tag activity / mRNA processing / transcription corepressor activity / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / microtubule cytoskeleton / cellular response to lipopolysaccharide / ATPase binding / ribosomal small subunit biogenesis / protein-macromolecule adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / ciliary basal body / cell division / intracellular membrane-bounded organelle / GTPase activity / centrosome / GTP binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Zhang Z / Kumar V / Dybkov O / Will CL / Urlaub H / Stark H / Luehrmann R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. Authors: Zhenwei Zhang / Vinay Kumar / Olexandr Dybkov / Cindy L Will / Henning Urlaub / Holger Stark / Reinhard Lührmann / ![]() ![]() Abstract: The B complex is a key intermediate stage of spliceosome assembly. To improve the structural resolution of monomeric, human spliceosomal B (hB) complexes and thereby generate a more comprehensive hB ...The B complex is a key intermediate stage of spliceosome assembly. To improve the structural resolution of monomeric, human spliceosomal B (hB) complexes and thereby generate a more comprehensive hB molecular model, we determined the cryo-EM structure of B complex dimers formed in the presence of ATP S. The enhanced resolution of these complexes allows a finer molecular dissection of how the 5' splice site (5'ss) is recognized in hB, and new insights into molecular interactions of FBP21, SNU23 and PRP38 with the U6/5'ss helix and with each other. It also reveals that SMU1 and RED are present as a heterotetrameric complex and are located at the interface of the B dimer protomers. We further show that MFAP1 and UBL5 form a 5' exon binding channel in hB, and elucidate the molecular contacts stabilizing the 5' exon at this stage. Our studies thus yield more accurate models of protein and RNA components of hB complexes. They further allow the localization of additional proteins and protein domains (such as SF3B6, BUD31 and TCERG1) whose position was not previously known, thereby uncovering new functions for B-specific and other hB proteins during pre-mRNA splicing. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 493.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 40.4 KB 40.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.3 KB | Display | ![]() |
Images | ![]() | 40.6 KB | ||
Filedesc metadata | ![]() | 13.2 KB | ||
Others | ![]() ![]() | 428.4 MB 428.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 882.6 KB | Display | ![]() |
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Full document | ![]() | 882.1 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8q7nMC ![]() 8qo9C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18225_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18225_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : human pre-catalytic spliceosome
+Supramolecule #1: human pre-catalytic spliceosome
+Macromolecule #1: U5 snRNA
+Macromolecule #2: U6 snRNA
+Macromolecule #11: MINX pre-mRNA
+Macromolecule #20: U4 snRNA
+Macromolecule #3: Splicing factor 3A subunit 1
+Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #5: Thioredoxin-like protein 4A
+Macromolecule #6: Pre-mRNA-splicing factor 38A
+Macromolecule #7: Microfibrillar-associated protein 1
+Macromolecule #8: NHP2-like protein 1, N-terminally processed
+Macromolecule #9: Protein BUD31 homolog
+Macromolecule #10: WW domain-binding protein 4
+Macromolecule #12: Zinc finger matrin-type protein 2
+Macromolecule #13: Ubiquitin-like protein 5
+Macromolecule #14: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #15: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #16: Pre-mRNA-processing factor 6
+Macromolecule #17: Pre-mRNA-processing-splicing factor 8
+Macromolecule #18: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #19: Transcription elongation regulator 1
+Macromolecule #21: U4/U6 small nuclear ribonucleoprotein Prp3
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |