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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 | |||||||||
![]() | The cryo-EM map of human C* complex | |||||||||
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Function / homology | ![]() second spliceosomal transesterification activity / 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 / spliceosomal complex disassembly / exon-exon junction complex / pre-mRNA 3'-splice site binding / granulocyte differentiation / post-mRNA release spliceosomal complex ...second spliceosomal transesterification activity / 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 / spliceosomal complex disassembly / exon-exon junction complex / pre-mRNA 3'-splice site binding / granulocyte differentiation / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / regulation of translation at postsynapse, modulating synaptic transmission / 3'-5' RNA helicase activity / U2 snRNP binding / negative regulation of toll-like receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / renal system process / generation of catalytic spliceosome for first transesterification step / intracellular mRNA localization / negative regulation of excitatory postsynaptic potential / U7 snRNP / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / histone pre-mRNA 3'end processing complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of interleukin-8 production / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / regulation of mRNA processing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / negative regulation of lipopolysaccharide-mediated signaling pathway / selenocysteine insertion sequence binding / Deadenylation of mRNA / embryonic brain development / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / negative regulation of phosphorylation / methylosome / negative regulation of interferon-beta production / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / U1 snRNP binding / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-end processing / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / ATP-dependent activity, acting on RNA / small nuclear ribonucleoprotein complex / embryonic cranial skeleton morphogenesis / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / commitment complex / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / telomerase RNA binding / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / U4 snRNP / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / positive regulation of alpha-beta T cell differentiation / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / U1 snRNP / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ubiquitin-ubiquitin ligase activity / exploration behavior / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / lipid biosynthetic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / hematopoietic stem cell proliferation / cyclosporin A binding / nuclear androgen receptor binding / negative regulation of type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / precatalytic spliceosome / Notch-HLH transcription pathway Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Zhan X / Lu Y / Shi Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of exon ligation by human spliceosome. Authors: Xiechao Zhan / Yichen Lu / Xiaofeng Zhang / Chuangye Yan / Yigong Shi / ![]() Abstract: Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C complex, which executes exon ligation. Here, we ...Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C-I and pre-C-II, both at 3.6 Å. In both structures, the 3' splice site is already docked into the active site, the ensuing 3' exon sequences are anchored on PRP8, and the step II factor FAM192A contacts the duplex between U2 snRNA and the branch site. In the transition of pre-C-I to pre-C-II, the step II factors Cactin, FAM32A, PRKRIP1, and SLU7 are recruited. Notably, the RNA helicase PRP22 is positioned quite differently in the pre-C-I, pre-C-II, and C complexes, suggesting a role in 3' exon binding and proofreading. Together with information on human C and C complexes, our studies recapitulate a molecular choreography of the C-to-C transition, revealing mechanistic insights into exon ligation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 230.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 66.7 KB 66.7 KB | Display Display | ![]() |
Images | ![]() | 65.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 471 KB | Display | ![]() |
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Full document | ![]() | 470.6 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w5bMC ![]() 7w59C ![]() 7w5aC 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 | The cryo-EM map of human C* complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.338 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Human pre-C*-I complex
+Supramolecule #1: Human pre-C*-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 #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: RNA helicase aquarius
+Macromolecule #19: SNW domain-containing protein 1
+Macromolecule #20: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #21: Pleiotropic regulator 1
+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: ATP-dependent RNA helicase DHX8
+Macromolecule #26: Cactin
+Macromolecule #27: PRKR-interacting protein 1
+Macromolecule #28: Protein FAM32A
+Macromolecule #29: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #30: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #31: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #32: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #33: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #34: Small nuclear ribonucleoprotein F
+Macromolecule #35: Small nuclear ribonucleoprotein E
+Macromolecule #36: Small nuclear ribonucleoprotein G
+Macromolecule #37: Pre-mRNA-processing factor 19
+Macromolecule #38: U2 small nuclear ribonucleoprotein A'
+Macromolecule #39: U2 small nuclear ribonucleoprotein B''
+Macromolecule #40: Pre-mRNA-splicing factor SLU7
+Macromolecule #41: Protein mago nashi homolog
+Macromolecule #42: RNA-binding protein 8A
+Macromolecule #43: Eukaryotic initiation factor 4A-III
+Macromolecule #44: Protein CASC3
+Macromolecule #45: NF-kappa-B-activating protein
+Macromolecule #2: U5 snRNA
+Macromolecule #6: U6 snRNA
+Macromolecule #7: Pre-mRNA
+Macromolecule #8: Pre-mRNA
+Macromolecule #9: U2 snRNA
+Macromolecule #46: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #47: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #48: MAGNESIUM ION
+Macromolecule #49: ZINC ION
+Macromolecule #50: ADENOSINE-5'-TRIPHOSPHATE
-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 K2 SUMMIT (4k 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: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58374 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |