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- EMDB-34507: Cryo-EM structure of human exon-defined spliceosome in the mature... -
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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 mature 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 / Post pre-B state / ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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 | ![]() | 478.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 72.8 KB 72.8 KB | Display Display | ![]() |
Images | ![]() | 278.9 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 20.7 KB | ||
Others | ![]() ![]() | 411 MB 410.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h6kMC ![]() 8h6eC ![]() 8h6jC ![]() 8h6lC C: citing same article ( M: atomic model generated by this map |
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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. | ||||||||||||||||||||
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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Density Histograms |
-Half map: #2
File | emd_34507_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_34507_half_map_2.map | ||||||||||||
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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: 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 | ![]() |
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
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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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 414060 |