+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32319 | |||||||||
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Title | The cryo-EM structure of human pre-C*-II complex | |||||||||
Map data | The cryo-EM map of human pre-C*-II complex | |||||||||
Sample |
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Function / homology | Function and homology information 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 / spliceosomal complex disassembly / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / pre-mRNA 3'-splice site binding / snRNP binding ...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 / spliceosomal complex disassembly / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / pre-mRNA 3'-splice site binding / snRNP binding / post-mRNA release spliceosomal complex / negative regulation of proteasomal protein catabolic process / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / negative regulation of toll-like receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / intracellular mRNA localization / 3'-5' RNA helicase activity / regulation of translation at postsynapse, modulating synaptic transmission / U7 snRNP / generation of catalytic spliceosome for first transesterification step / renal system process / negative regulation of excitatory postsynaptic potential / histone pre-mRNA 3'end processing complex / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / negative regulation of interleukin-8 production / regulation of mRNA processing / negative regulation of lipopolysaccharide-mediated signaling pathway / Deadenylation of mRNA / embryonic brain development / negative regulation of phosphorylation / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / negative regulation of interferon-beta production / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / Prp19 complex / RNA splicing, via transesterification reactions / poly(A) binding / positive regulation of androgen receptor activity / M-decay: degradation of maternal mRNAs by maternally stored factors / spliceosomal tri-snRNP complex / RNA stem-loop binding / mRNA 3'-end processing / small nuclear ribonucleoprotein complex / pre-mRNA binding / P granule / sno(s)RNA-containing ribonucleoprotein complex / ATP-dependent activity, acting on RNA / SMN-Sm protein complex / embryonic cranial skeleton morphogenesis / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / telomerase holoenzyme complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / positive regulation by host of viral transcription / U4 snRNP / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / U2 snRNP / nuclear vitamin D receptor binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA Polymerase II Transcription Termination / RUNX3 regulates NOTCH signaling / U1 snRNP / NOTCH4 Intracellular Domain Regulates Transcription / U2-type prespliceosome / ubiquitin-ubiquitin ligase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exploration behavior / K63-linked polyubiquitin modification-dependent protein binding / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / lipid biosynthetic process / precatalytic spliceosome / nuclear androgen receptor binding / negative regulation of type I interferon-mediated signaling pathway / cyclosporin A binding / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / negative regulation of NF-kappaB transcription factor activity / protein kinase inhibitor activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) / unidentified adenovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Zhan X / Lu Y / Shi Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Mol Cell / Year: 2022 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 | emd_32319.map.gz | 230.2 MB | EMDB map data format | |
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Header (meta data) | emd-32319-v30.xml emd-32319.xml | 63.6 KB 63.6 KB | Display Display | EMDB header |
Images | emd_32319.png | 68.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32319 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32319 | HTTPS FTP |
-Related structure data
Related structure data | 7w5aMC 7w59C 7w5bC 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_32319.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The cryo-EM map of human pre-C*-II 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
-Sample components
+Entire : Human pre-C*-II complex
+Supramolecule #1: Human pre-C*-II complex
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #3: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #4: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #9: Pre-mRNA-splicing factor SYF1
+Macromolecule #10: Crooked neck-like protein 1
+Macromolecule #11: Pre-mRNA-splicing factor SPF27
+Macromolecule #12: Cell division cycle 5-like protein
+Macromolecule #13: Pre-mRNA-splicing factor SYF2
+Macromolecule #14: Protein BUD31 homolog
+Macromolecule #15: Pre-mRNA-splicing factor RBM22
+Macromolecule #16: Spliceosome-associated protein CWC15 homolog
+Macromolecule #17: RNA helicase aquarius
+Macromolecule #18: SNW domain-containing protein 1
+Macromolecule #19: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #20: Pleiotropic regulator 1
+Macromolecule #21: Serine/arginine repetitive matrix protein 2
+Macromolecule #22: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #23: Pre-mRNA-processing factor 17
+Macromolecule #24: PSME3-interacting protein
+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: Protein mago nashi homolog
+Macromolecule #38: RNA-binding protein 8A
+Macromolecule #39: Eukaryotic initiation factor 4A-III
+Macromolecule #40: Protein CASC3
+Macromolecule #41: Pre-mRNA-processing factor 19
+Macromolecule #42: U2 small nuclear ribonucleoprotein A'
+Macromolecule #43: U2 small nuclear ribonucleoprotein B''
+Macromolecule #44: Pre-mRNA-splicing factor SLU7
+Macromolecule #2: U5 snRNA
+Macromolecule #5: U6 snRNA
+Macromolecule #6: Pre-mRNA
+Macromolecule #7: Pre-mRNA
+Macromolecule #8: U2 snRNA
+Macromolecule #45: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #46: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #47: MAGNESIUM ION
+Macromolecule #48: ZINC ION
+Macromolecule #49: ADENOSINE-5'-TRIPHOSPHATE
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212224 |