+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18529 | |||||||||
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Title | Cryo-EM structure of a human spliceosomal B complex protomer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | spliceosome / SPLICING | |||||||||
Function / homology | Function and homology information DNA topoisomerase binding / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization ...DNA topoisomerase binding / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / protein kinase B binding / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA binding / U11/U12 snRNP / PH domain binding / dense fibrillar component / U2 snRNP binding / alternative mRNA splicing, via spliceosome / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / 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 / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / transcription elongation factor activity / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / snRNP binding / U1 snRNP binding / mRNA 3'-end processing / protein localization to kinetochore / P-body assembly / blastocyst formation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / proline-rich region binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / commitment complex / U2-type prespliceosome assembly / RNA polymerase binding / U2-type catalytic step 2 spliceosome / ubiquitin-like protein conjugating enzyme binding / positive regulation of mRNA splicing, via spliceosome / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / RNA Polymerase II Transcription Termination / SAGA complex / U3 snoRNA binding / positive regulation of transcription by RNA polymerase III / U1 snRNP / positive regulation of protein targeting to mitochondrion / tRNA processing / Cajal body / U2-type prespliceosome / cyclosporin A binding / regulation of alternative mRNA splicing, via spliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / mitotic spindle assembly checkpoint signaling / positive regulation of transcription by RNA polymerase I / oligodendrocyte differentiation / spliceosomal complex assembly / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA catabolic process / mRNA 5'-splice site recognition / nuclear-transcribed mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-splice site recognition / protein peptidyl-prolyl isomerization / MLL1 complex / spliceosomal tri-snRNP complex assembly Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.29 Å | |||||||||
Authors | Zhang Z / Kumar V / Dybkov O / Will CL / Urlaub H / Stark H / Luehrmann R | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: EMBO J / Year: 2024 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 | emd_18529.map.gz | 51 MB | EMDB map data format | |
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Header (meta data) | emd-18529-v30.xml emd-18529.xml | 78.7 KB 78.7 KB | Display Display | EMDB header |
Images | emd_18529.png | 74.8 KB | ||
Filedesc metadata | emd-18529.cif.gz | 21.6 KB | ||
Others | emd_18529_half_map_1.map.gz emd_18529_half_map_2.map.gz | 51.6 MB 51.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18529 | HTTPS FTP |
-Related structure data
Related structure data | 8qo9MC 8q7nC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18529.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.32 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18529_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18529_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human spliceosomal B complex
+Supramolecule #1: human spliceosomal B complex
+Macromolecule #1: Splicing factor 3B subunit 4
+Macromolecule #2: Splicing factor 3A subunit 2
+Macromolecule #3: Splicing factor 3A subunit 3
+Macromolecule #4: Splicing factor 3B subunit 2
+Macromolecule #5: Splicing factor 3B subunit 5
+Macromolecule #7: Splicing factor 3B subunit 3
+Macromolecule #8: PHD finger-like domain-containing protein 5A
+Macromolecule #9: Splicing factor 3B subunit 1
+Macromolecule #10: Splicing factor 3B subunit 6
+Macromolecule #11: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #12: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #13: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #14: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #15: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #16: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #17: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #18: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #20: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #21: Small nuclear ribonucleoprotein F
+Macromolecule #22: Small nuclear ribonucleoprotein E
+Macromolecule #23: Small nuclear ribonucleoprotein G
+Macromolecule #24: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #25: U2 small nuclear ribonucleoprotein B''
+Macromolecule #26: U2 small nuclear ribonucleoprotein A'
+Macromolecule #27: Splicing factor 3A subunit 1
+Macromolecule #28: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #29: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #30: Protein Red
+Macromolecule #31: WD40 repeat-containing protein SMU1
+Macromolecule #32: Serine/arginine-rich splicing factor 1
+Macromolecule #33: Peptidyl-prolyl cis-trans isomerase H
+Macromolecule #35: Protein BUD31 homolog
+Macromolecule #36: Thioredoxin-like protein 4A
+Macromolecule #37: WW domain-binding protein 4
+Macromolecule #38: Microfibrillar-associated protein 1
+Macromolecule #40: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #41: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #42: Pre-mRNA-processing factor 6
+Macromolecule #43: Pre-mRNA-processing-splicing factor 8
+Macromolecule #44: Pre-mRNA-splicing factor 38A
+Macromolecule #45: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #46: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #47: NHP2-like protein 1, N-terminally processed
+Macromolecule #48: Transcription elongation regulator 1
+Macromolecule #51: Zinc finger matrin-type protein 2
+Macromolecule #52: U4/U6 small nuclear ribonucleoprotein Prp3
+Macromolecule #53: Ubiquitin-like protein 5
+Macromolecule #6: U2 snRNA
+Macromolecule #34: U5 snRNA
+Macromolecule #39: MINX pre-mRNA
+Macromolecule #49: U4 snRNA
+Macromolecule #50: U6 snRNA
-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: FEI FALCON III (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: ad initio |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50321 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |