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Yorodumi- EMDB-34507: Cryo-EM structure of human exon-defined spliceosome in the mature... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34507 | |||||||||
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Title | Cryo-EM structure of human exon-defined spliceosome in the mature B state. | |||||||||
Map data | Author stated: Some sections of the map have very low resolution. For these areas, only the C-alpha model was docked into the density. | |||||||||
Sample |
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Keywords | Exon-defined spliceosome / Post pre-B state / SPLICING | |||||||||
Function / homology | Function and homology information microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization ...microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / 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 / U11/U12 snRNP / U6 snRNP / box C/D sno(s)RNA binding / positive regulation of primary miRNA processing / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / dense fibrillar component / 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 / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / P-body assembly / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / U1 snRNP binding / blastocyst formation / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / U4 snRNA binding / telomerase holoenzyme complex / box C/D methylation guide snoRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / proline-rich region binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / rRNA modification in the nucleus and cytosol / box C/D snoRNP assembly / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / tRNA processing / U1 snRNP / positive regulation of protein targeting to mitochondrion / U3 snoRNA binding / U2-type prespliceosome / nuclear-transcribed mRNA catabolic process / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of miRNA metabolic process / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / mRNA catabolic process / regulation of RNA splicing / 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 / positive regulation of viral genome replication / U5 snRNP / RNA processing / U2 snRNA binding / regulation of DNA repair / U6 snRNA binding / spliceosomal snRNP assembly / protein peptidyl-prolyl isomerization / ribonucleoprotein complex binding / pre-mRNA intronic binding / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Zhang W / Zhan X / Zhang X / Bai R / Lei J / Yan C / Shi Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2024 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 | emd_34507.map.gz | 478.8 MB | EMDB map data format | |
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Header (meta data) | emd-34507-v30.xml emd-34507.xml | 72.8 KB 72.8 KB | Display Display | EMDB header |
Images | emd_34507.png | 278.9 KB | ||
Masks | emd_34507_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-34507.cif.gz | 20.7 KB | ||
Others | emd_34507_half_map_1.map.gz emd_34507_half_map_2.map.gz | 411 MB 410.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34507 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34507 | HTTPS FTP |
-Validation report
Summary document | emd_34507_validation.pdf.gz | 907.7 KB | Display | EMDB validaton report |
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Full document | emd_34507_full_validation.pdf.gz | 907.2 KB | Display | |
Data in XML | emd_34507_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_34507_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34507 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34507 | HTTPS FTP |
-Related structure data
Related structure data | 8h6kMC 8h6eC 8h6jC 8h6lC C: citing same article (ref.) M: atomic model generated by this map |
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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_34507.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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. | ||||||||||||||||||||
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
File | emd_34507_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34507_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34507_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : exon-defined post pre-B spliceosome
+Supramolecule #1: exon-defined post pre-B spliceosome
+Macromolecule #1: pre-mRNA
+Macromolecule #2: U5 snRNA
+Macromolecule #14: U6 snRNA
+Macromolecule #22: U4 snRNA
+Macromolecule #37: U2 snRNA
+Macromolecule #3: Pre-mRNA-processing-splicing factor 8
+Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #5: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #6: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #7: Isoform SM-B of Small nuclear ribonucleoprotein-associated protei...
+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 #13: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #15: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #16: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #17: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #18: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #19: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #20: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #21: U6 snRNA-associated Sm-like protein LSm8
+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: Peptidyl-prolyl cis-trans isomerase H
+Macromolecule #30: WW domain-binding protein 4
+Macromolecule #31: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #32: Microfibrillar-associated protein 1
+Macromolecule #33: Pre-mRNA-splicing factor 38A
+Macromolecule #34: Ubiquitin-like protein 5
+Macromolecule #35: Zinc finger matrin-type protein 2
+Macromolecule #36: WD40 repeat-containing protein SMU1
+Macromolecule #38: U2 small nuclear ribonucleoprotein A'
+Macromolecule #39: U2 small nuclear ribonucleoprotein B''
+Macromolecule #40: Splicing factor 3A subunit 1
+Macromolecule #41: Splicing factor 3A subunit 2
+Macromolecule #42: Splicing factor 3A subunit 3
+Macromolecule #43: Splicing factor 3B subunit 1
+Macromolecule #44: Splicing factor 3B subunit 2
+Macromolecule #45: Splicing factor 3B subunit 3
+Macromolecule #46: Splicing factor 3B subunit 4
+Macromolecule #47: Splicing factor 3B subunit 6
+Macromolecule #48: PHD finger-like domain-containing protein 5A
+Macromolecule #49: Splicing factor 3B subunit 5
+Macromolecule #50: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #51: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #52: MAGNESIUM ION
+Macromolecule #53: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 414060 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |