+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35107 | |||||||||
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Title | The cryo-EM structure of human Bact-I complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | spliceosome / Bact-I complex / RNA splicing / PRP2 / activation / SPLICING | |||||||||
Function / homology | Function and homology information RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding ...RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / generation of catalytic spliceosome for first transesterification step / B-WICH complex / regulation of vitamin D receptor signaling pathway / 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 / miRNA processing / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / poly(A) binding / positive regulation of androgen receptor activity / Prp19 complex / U1 snRNP binding / snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / transcription regulator inhibitor activity / positive regulation of vitamin D receptor signaling pathway / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / SAGA complex / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / Basigin interactions / U2 snRNP / NOTCH4 Intracellular Domain Regulates Transcription / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / positive regulation of neurogenesis / ubiquitin-ubiquitin ligase activity / pattern recognition receptor activity / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / U2-type prespliceosome / nuclear androgen receptor binding / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / SMAD binding / regulation of RNA splicing / mRNA 3'-splice site recognition / blastocyst development / protein peptidyl-prolyl isomerization / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / U5 snRNP / RHOBTB2 GTPase cycle / positive regulation of G1/S transition of mitotic cell cycle Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / unidentified adenovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Zhan X / Lu Y / Shi Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Molecular basis for the activation of human spliceosome. Authors: Xiechao Zhan / Yichen Lu / Yigong Shi / Abstract: The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic ...The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic spliceosome (B complex) into the activated spliceosome (B complex) and the catalytically activated spliceosome (B complex), involves major flux of protein components and structural rearrangements. Relying on a splicing inhibitor, we have captured six intermediate states between the B and B complexes: pre-B, B-I, B-II, B-III, B-IV, and post-B. Their cryo-EM structures, together with an improved structure of the catalytic step I spliceosome (C complex), reveal how the catalytic center matures around the internal stem loop of U6 snRNA, how the branch site approaches 5'-splice site, how the RNA helicase PRP2 rearranges to bind pre-mRNA, and how U2 snRNP undergoes remarkable movement to facilitate activation. We identify a previously unrecognized key role of PRP2 in spliceosome activation. Our study recapitulates a molecular choreography of the human spliceosome during its catalytic activation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35107.map.gz | 398.9 MB | EMDB map data format | |
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Header (meta data) | emd-35107-v30.xml emd-35107.xml | 81.5 KB 81.5 KB | Display Display | EMDB header |
Images | emd_35107.png | 98.4 KB | ||
Filedesc metadata | emd-35107.cif.gz | 24.7 KB | ||
Others | emd_35107_half_map_1.map.gz emd_35107_half_map_2.map.gz | 391.1 MB 391.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35107 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35107 | HTTPS FTP |
-Validation report
Summary document | emd_35107_validation.pdf.gz | 925.9 KB | Display | EMDB validaton report |
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Full document | emd_35107_full_validation.pdf.gz | 925.4 KB | Display | |
Data in XML | emd_35107_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_35107_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35107 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35107 | HTTPS FTP |
-Related structure data
Related structure data | 8i0rMC 8i0pC 8i0sC 8i0tC 8i0uC 8i0vC 8i0wC 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_35107.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.077 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35107_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35107_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The human Bact-I complex
+Supramolecule #1: The human Bact-I complex
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #3: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #4: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #5: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #9: Pre-mRNA-splicing factor SYF1
+Macromolecule #10: Crooked neck-like protein 1
+Macromolecule #11: RING finger protein 113A
+Macromolecule #12: Cell division cycle 5-like protein
+Macromolecule #13: Protein BUD31 homolog
+Macromolecule #14: Pre-mRNA-splicing factor RBM22
+Macromolecule #15: Spliceosome-associated protein CWC15 homolog
+Macromolecule #16: RNA helicase aquarius
+Macromolecule #17: SNW domain-containing protein 1
+Macromolecule #18: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
+Macromolecule #19: Pleiotropic regulator 1
+Macromolecule #20: Serine/arginine repetitive matrix protein 2
+Macromolecule #21: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #22: Unknown polymer
+Macromolecule #23: Smad nuclear-interacting protein 1
+Macromolecule #24: RNA-binding motif protein, X-linked 2
+Macromolecule #25: BUD13 homolog
+Macromolecule #26: Splicing factor 3B subunit 1
+Macromolecule #27: Splicing factor 3B subunit 3
+Macromolecule #28: U2 small nuclear ribonucleoprotein B''
+Macromolecule #29: Splicing factor 3A subunit 3
+Macromolecule #30: Splicing factor 3A subunit 1
+Macromolecule #31: Splicing factor 3B subunit 2
+Macromolecule #32: Splicing factor 3B subunit 4
+Macromolecule #33: Splicing factor 3B subunit 6
+Macromolecule #34: PHD finger-like domain-containing protein 5A
+Macromolecule #35: Splicing factor 3B subunit 5
+Macromolecule #36: RING-type E3 ubiquitin-protein ligase PPIL2
+Macromolecule #37: Serine/arginine repetitive matrix protein 1
+Macromolecule #38: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #39: Splicing factor 3A subunit 2
+Macromolecule #40: U2 small nuclear ribonucleoprotein A'
+Macromolecule #41: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #42: Small nuclear ribonucleoprotein F
+Macromolecule #43: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #44: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #45: Small nuclear ribonucleoprotein G
+Macromolecule #46: Small nuclear ribonucleoprotein E
+Macromolecule #47: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #48: Peptidyl-prolyl cis-trans isomerase CWC27 homolog
+Macromolecule #2: U5 snRNA
+Macromolecule #6: U6 snRNA
+Macromolecule #7: pre-mRNA
+Macromolecule #8: U2 snRNA
+Macromolecule #49: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #50: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #51: MAGNESIUM ION
+Macromolecule #52: ZINC ION
-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 / Chamber humidity: 100 % |
-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: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136665 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |