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- EMDB-34500: Cryo-EM structure of human exon-defined spliceosome in the late p... -
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Open data
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Basic information
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Title | Cryo-EM structure of human exon-defined spliceosome in the late pre-B state. | |||||||||
![]() | Author stated: Some sections of the map have very low resolution. For these areas, only the C-alpha model was docked into the density. | |||||||||
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![]() | exon-defined spliceosome / late pre-B state / RNA splicing / SPLICING | |||||||||
Function / homology | ![]() 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 / positive regulation of hippo signaling / RNA localization / R-loop processing ...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 / positive regulation of hippo signaling / RNA localization / R-loop processing / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / regulation of mitotic cell cycle spindle assembly checkpoint / 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 / P-body assembly / pICln-Sm protein complex / blastocyst formation / 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 / 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 / U4 snRNP / box C/D snoRNP assembly / 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 / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / mRNA 3'-splice site recognition / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / 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 / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of protein export from nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Zhang W / Zhan X / Zhang X / Bai R / Lei J / Yan C / Shi Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into human exon-defined spliceosome prior to activation. Authors: Wenyu Zhang / Xiaofeng Zhang / Xiechao Zhan / Rui Bai / Jianlin Lei / Chuangye Yan / Yigong Shi / ![]() Abstract: Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, ...Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 483.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 73.7 KB 73.7 KB | Display Display | ![]() |
Images | ![]() | 152.4 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 21.1 KB | ||
Others | ![]() ![]() | 475.7 MB 475.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h6eMC ![]() 8h6jC ![]() 8h6kC ![]() 8h6lC 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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Annotation | Author stated: Some sections of the map have very low resolution. For these areas, only the C-alpha model was docked into the density. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34500_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34500_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : exon-defined post pre-B spliceosome
+Supramolecule #1: exon-defined post pre-B spliceosome
+Macromolecule #1: pre-mRNA
+Macromolecule #2: U6 snRNA
+Macromolecule #10: U5 snRNA
+Macromolecule #22: U4 snRNA
+Macromolecule #35: U2 snRNA
+Macromolecule #3: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #4: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #5: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #6: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #7: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #8: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #9: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #11: Pre-mRNA-processing-splicing factor 8
+Macromolecule #12: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #13: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #14: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #15: Isoform SM-B of Small nuclear ribonucleoprotein-associated protei...
+Macromolecule #16: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #17: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #18: Small nuclear ribonucleoprotein F
+Macromolecule #19: Small nuclear ribonucleoprotein E
+Macromolecule #20: Small nuclear ribonucleoprotein G
+Macromolecule #21: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #23: U4/U6 small nuclear ribonucleoprotein Prp3
+Macromolecule #24: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #25: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #26: NHP2-like protein 1
+Macromolecule #27: Thioredoxin-like protein 4A
+Macromolecule #28: Pre-mRNA-processing factor 6
+Macromolecule #29: RNA-binding protein 42
+Macromolecule #30: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #31: U4/U6.U5 tri-snRNP-associated protein 2
+Macromolecule #32: Probable ATP-dependent RNA helicase DDX23
+Macromolecule #33: U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
+Macromolecule #34: Serine/threonine-protein kinase PRP4 homolog
+Macromolecule #36: U2 small nuclear ribonucleoprotein A'
+Macromolecule #37: U2 small nuclear ribonucleoprotein B''
+Macromolecule #38: Splicing factor 3A subunit 1
+Macromolecule #39: Splicing factor 3A subunit 2
+Macromolecule #40: Splicing factor 3A subunit 3
+Macromolecule #41: Splicing factor 3B subunit 1
+Macromolecule #42: Splicing factor 3B subunit 2
+Macromolecule #43: Splicing factor 3B subunit 3
+Macromolecule #44: Splicing factor 3B subunit 4
+Macromolecule #45: Splicing factor 3B subunit 6
+Macromolecule #46: PHD finger-like domain-containing protein 5A
+Macromolecule #47: Splicing factor 3B subunit 5
+Macromolecule #48: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #49: MAGNESIUM ION
+Macromolecule #50: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #51: ZINC ION
-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: 8 |
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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: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140426 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |