+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18781 | |||||||||
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Title | Cryo-EM structure of the cross-exon B-like complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | spliceosome / SPLICING | |||||||||
Function / homology | Function and homology information 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 / U4atac snRNA 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 / 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 / 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 / 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 / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / 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 / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / 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 / 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 / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / mRNA 3'-splice site recognition / protein peptidyl-prolyl isomerization / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / positive regulation of viral genome replication / U2 snRNA binding / RNA processing / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of DNA repair / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Zhang Z / Kumar V / Dybkov O / Will CL / Zhong J / Ludwig S / Urlaub H / Kastner B / Stark H / Luehrmann R | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nature / Year: 2024 Title: Structural insights into the cross-exon to cross-intron spliceosome switch. Authors: Zhenwei Zhang / Vinay Kumar / Olexandr Dybkov / Cindy L Will / Jiayun Zhong / Sebastian E J Ludwig / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / Abstract: Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur ...Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur through an exon-defined pathway, whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5' splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex. Exon definition promotes the splicing of upstream introns and plays a key part in alternative splicing regulation. However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5' splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18781.map.gz | 193 MB | EMDB map data format | |
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Header (meta data) | emd-18781-v30.xml emd-18781.xml | 76.3 KB 76.3 KB | Display Display | EMDB header |
Images | emd_18781.png | 53.4 KB | ||
Filedesc metadata | emd-18781.cif.gz | 20.9 KB | ||
Others | emd_18781_half_map_1.map.gz emd_18781_half_map_2.map.gz | 193.4 MB 193.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18781 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18781 | HTTPS FTP |
-Validation report
Summary document | emd_18781_validation.pdf.gz | 863.3 KB | Display | EMDB validaton report |
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Full document | emd_18781_full_validation.pdf.gz | 862.9 KB | Display | |
Data in XML | emd_18781_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_18781_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18781 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18781 | HTTPS FTP |
-Related structure data
Related structure data | 8qzsMC 8qozC 8qp8C 8qp9C 8qpaC 8qpbC 8qpeC 8qpkC 8qxdC 8r08C 8r09C 8r0aC 8r0bC 8rm5C 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_18781.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18781_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18781_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human spliceosomal cross-exon B-like complex
+Supramolecule #1: human spliceosomal cross-exon B-like complex
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #2: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #7: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #8: Thioredoxin-like protein 4A
+Macromolecule #9: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #10: Pre-mRNA-splicing factor 38A
+Macromolecule #11: NHP2-like protein 1, N-terminally processed
+Macromolecule #12: Ubiquitin carboxyl-terminal hydrolase 39
+Macromolecule #13: Peptidyl-prolyl cis-trans isomerase H
+Macromolecule #14: WW domain-binding protein 4
+Macromolecule #16: Splicing factor 3A subunit 1
+Macromolecule #17: Zinc finger matrin-type protein 2
+Macromolecule #18: Splicing factor 3B subunit 4
+Macromolecule #19: Splicing factor 3A subunit 2
+Macromolecule #20: Splicing factor 3A subunit 3
+Macromolecule #21: Splicing factor 3B subunit 2
+Macromolecule #22: Splicing factor 3B subunit 5
+Macromolecule #23: Splicing factor 3B subunit 3
+Macromolecule #24: PHD finger-like domain-containing protein 5A
+Macromolecule #25: Splicing factor 3B subunit 1
+Macromolecule #26: Splicing factor 3B subunit 6
+Macromolecule #27: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #28: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #29: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #30: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #31: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #32: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #33: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #34: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #35: Small nuclear ribonucleoprotein F
+Macromolecule #36: Small nuclear ribonucleoprotein E
+Macromolecule #37: Small nuclear ribonucleoprotein G
+Macromolecule #38: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #39: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #40: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #41: U2 small nuclear ribonucleoprotein B''
+Macromolecule #42: U2 small nuclear ribonucleoprotein A'
+Macromolecule #43: Protein Red
+Macromolecule #44: WD40 repeat-containing protein SMU1
+Macromolecule #45: Microfibrillar-associated protein 1
+Macromolecule #48: U4/U6 small nuclear ribonucleoprotein Prp3
+Macromolecule #49: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #50: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #51: Pre-mRNA-processing factor 6
+Macromolecule #52: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #3: U5 snRNA
+Macromolecule #4: U2 snRNA
+Macromolecule #5: U6 snRNA
+Macromolecule #6: U4 snRNA
+Macromolecule #15: Pre-mRNA
+Macromolecule #46: Oligo 1
+Macromolecule #47: Oligo 2
-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: ab initio |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 334084 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |