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Open data
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Basic information
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Title | The cryo-EM structure of human C complex | |||||||||
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![]() | spliceosome / RNA splicing / PRP16 / branching / SPLICING | |||||||||
Function / homology | ![]() striated muscle dense body / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / post-spliceosomal complex / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway ...striated muscle dense body / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / post-spliceosomal complex / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / negative regulation of excitatory postsynaptic potential / U2 snRNP binding / intracellular mRNA localization / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / U7 snRNP / generation of catalytic spliceosome for first transesterification step / regulation of vitamin D receptor signaling pathway / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / positive regulation of androgen receptor activity / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Deadenylation of mRNA / nuclear retinoic acid receptor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / embryonic brain development / U12-type spliceosomal complex / protein methylation / methylosome / 7-methylguanosine cap hypermethylation / Prp19 complex / poly(A) binding / U1 snRNP binding / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-end processing / sno(s)RNA-containing ribonucleoprotein complex / RNA splicing, via transesterification reactions / pICln-Sm protein complex / embryonic cranial skeleton morphogenesis / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / pre-mRNA binding / C2H2 zinc finger domain binding / snRNP binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / telomerase RNA binding / telomerase holoenzyme complex / spliceosomal tri-snRNP complex / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / positive regulation of vitamin D receptor signaling pathway / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / P granule / nuclear vitamin D receptor binding / commitment complex / U2-type prespliceosome assembly / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / U2-type catalytic step 2 spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / positive regulation of mRNA splicing, via spliceosome / RUNX3 regulates NOTCH signaling / U4 snRNP / NOTCH4 Intracellular Domain Regulates Transcription / U2 snRNP / RNA Polymerase II Transcription Termination / exploration behavior / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U1 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / positive regulation of neurogenesis / U2-type prespliceosome / lipid biosynthetic process / inner cell mass cell proliferation / cyclosporin A binding / regulation of alternative mRNA splicing, via spliceosome / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / muscle organ development / precatalytic spliceosome / Notch-HLH transcription pathway / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / mitotic G2 DNA damage checkpoint signaling / associative learning / negative regulation of DNA damage response, signal transduction by p53 class mediator / mRNA 3'-splice site recognition Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Zhan X / Lu Y / Shi Y | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 398.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 75.3 KB 75.3 KB | Display Display | ![]() |
Images | ![]() | 85.2 KB | ||
Filedesc metadata | ![]() | 22.9 KB | ||
Others | ![]() ![]() | 392 MB 392 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i0wMC ![]() 8i0pC ![]() 8i0rC ![]() 8i0sC ![]() 8i0tC ![]() 8i0uC ![]() 8i0vC 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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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_35113_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35113_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : The human Bact-III complex
+Supramolecule #1: The human Bact-III 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 #10: Pre-mRNA-splicing factor SYF1
+Macromolecule #11: Crooked neck-like protein 1
+Macromolecule #12: Pre-mRNA-splicing factor SPF27
+Macromolecule #13: Cell division cycle 5-like protein
+Macromolecule #14: Pre-mRNA-splicing factor SYF2
+Macromolecule #15: Protein BUD31 homolog
+Macromolecule #16: Pre-mRNA-splicing factor RBM22
+Macromolecule #17: Spliceosome-associated protein CWC15 homolog
+Macromolecule #18: SNW domain-containing protein 1
+Macromolecule #19: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #20: Pleiotropic regulator 1
+Macromolecule #21: RNA helicase aquarius
+Macromolecule #22: Serine/arginine repetitive matrix protein 2
+Macromolecule #23: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #24: Pre-mRNA-processing factor 17
+Macromolecule #25: Pre-mRNA-splicing factor CWC25 homolog
+Macromolecule #26: Coiled-coil domain-containing protein 94
+Macromolecule #27: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
+Macromolecule #28: Pre-mRNA-processing factor 19
+Macromolecule #29: Eukaryotic initiation factor 4A-III
+Macromolecule #30: Protein mago nashi homolog
+Macromolecule #31: RNA-binding protein 8A
+Macromolecule #32: Protein CASC3
+Macromolecule #33: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #34: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #35: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #36: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #37: Small nuclear ribonucleoprotein F
+Macromolecule #38: Small nuclear ribonucleoprotein E
+Macromolecule #39: Small nuclear ribonucleoprotein G
+Macromolecule #40: U2 small nuclear ribonucleoprotein A'
+Macromolecule #41: U2 small nuclear ribonucleoprotein B''
+Macromolecule #42: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #43: Pre-mRNA-splicing factor ISY1 homolog
+Macromolecule #44: Peptidylprolyl isomerase domain and WD repeat-containing protein 1
+Macromolecule #45: Corepressor interacting with RBPJ 1
+Macromolecule #46: WD repeat-containing protein 70
+Macromolecule #47: Protein FRG1
+Macromolecule #48: UNK
+Macromolecule #2: U5 snRNA
+Macromolecule #6: U6 snRNA
+Macromolecule #7: pre-mRNA
+Macromolecule #8: pre-mRNA
+Macromolecule #9: 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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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) / Detector mode: SUPER-RESOLUTION / 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: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18223 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |