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Yorodumi- EMDB-6864: The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C co... -
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-Basic information
Entry | Database: EMDB / ID: EMD-6864 | ||||||||||||
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Title | The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution | ||||||||||||
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Sample |
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Function / homology | Function and homology information exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex ...exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / intracellular mRNA localization / histone pre-mRNA DCP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNP / 3'-5' RNA helicase activity / regulation of translation at postsynapse, modulating synaptic transmission / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / negative regulation of excitatory postsynaptic potential / 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 / regulation of mRNA processing / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / Deadenylation of mRNA / embryonic brain development / methylosome / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / pre-mRNA binding / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / Prp19 complex / poly(A) binding / positive regulation of androgen receptor activity / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / M-decay: degradation of maternal mRNAs by maternally stored factors / P granule / RNA stem-loop binding / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / embryonic cranial skeleton morphogenesis / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / positive regulation by host of viral transcription / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / U2 snRNP / Notch binding / nuclear vitamin D receptor binding / RNA Polymerase II Transcription Termination / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U1 snRNP / RUNX3 regulates NOTCH signaling / U2-type prespliceosome / NOTCH4 Intracellular Domain Regulates Transcription / K63-linked polyubiquitin modification-dependent protein binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ubiquitin-ubiquitin ligase activity / exploration behavior / lipid biosynthetic process / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / protein K63-linked ubiquitination / mitotic G2 DNA damage checkpoint signaling / negative regulation of DNA damage response, signal transduction by p53 class mediator / mRNA 3'-splice site recognition / associative learning / blastocyst development Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Zhan X / Yan C / Zhang X / Lei J / Shi Y | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Science / Year: 2018 Title: Structure of a human catalytic step I spliceosome. Authors: Xiechao Zhan / Chuangye Yan / Xiaofeng Zhang / Jianlin Lei / Yigong Shi / Abstract: Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron ...Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron microscopy structure of the human C complex at an average resolution of 4.1 angstroms. Compared with the C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in , respectively) closely interact with the DEAH-family adenosine triphosphatase/helicase Prp16 and bridge the gap between Prp16 and the active-site RNA elements. These features, together with structural comparison of the human C and C* complexes, provide mechanistic insights into ribonucleoprotein remodeling and allow the proposition of a working mechanism for the C-to-C* transition. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6864.map.gz | 228.3 MB | EMDB map data format | |
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Header (meta data) | emd-6864-v30.xml emd-6864.xml | 76.8 KB 76.8 KB | Display Display | EMDB header |
Images | emd_6864.png | 296.8 KB | ||
Others | emd_6864_additional.map.gz emd_6864_half_map_1.map.gz emd_6864_half_map_2.map.gz | 223.7 MB 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6864 | HTTPS FTP |
-Related structure data
Related structure data | 5yzgMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6864.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.338 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_6864_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_6864_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_6864_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human Catalytic Step I Spliceosome
+Supramolecule #1: Human Catalytic Step I Spliceosome
+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: Pre-mRNA-splicing factor SPF27
+Macromolecule #12: Cell division cycle 5-like protein
+Macromolecule #13: Pre-mRNA-splicing factor ISY1 homolog
+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: Intron-binding protein 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 2
+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: Peptidylprolyl isomerase domain and WD repeat-containing protein 1
+Macromolecule #44: Peptidyl-prolyl cis-trans isomerase G
+Macromolecule #45: UNKNOW
+Macromolecule #2: U5 snRNA
+Macromolecule #6: U6 snRNA
+Macromolecule #7: Pre-mRNA
+Macromolecule #8: U2 snRNA
+Macromolecule #46: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #47: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #48: MAGNESIUM ION
+Macromolecule #49: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #50: ZINC ION
+Macromolecule #51: 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 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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
Particle selection | Number selected: 1464033 |
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CTF correction | Software - Name: Gctf (ver. 0.66) |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final 3D classification | Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 53633 |