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Yorodumi- EMDB-3545: Cryo-EM structure of a human spliceosome activated for step 2 of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3545 | |||||||||
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Title | Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex) | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information 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 / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding ...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 / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / 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 / 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 / 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 / ATP-dependent activity, acting on RNA / 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 / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / protein K63-linked ubiquitination / mitotic G2 DNA damage checkpoint signaling / associative learning / blastocyst development / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / gastrulation / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNP Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||
Authors | Bertram K / Liu WT | |||||||||
Citation | Journal: Nature / Year: 2017 Title: Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Authors: Karl Bertram / Dmitry E Agafonov / Wen-Ti Liu / Olexandr Dybkov / Cindy L Will / Klaus Hartmuth / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / Abstract: Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human ...Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 Å, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 Å from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP. | |||||||||
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_3545.map.gz | 164.8 MB | EMDB map data format | |
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Header (meta data) | emd-3545-v30.xml emd-3545.xml | 57.8 KB 57.8 KB | Display Display | EMDB header |
Images | emd_3545.png | 46.8 KB | ||
Others | emd_3545_half_map_1.map.gz emd_3545_half_map_2.map.gz | 139.4 MB 139.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3545 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3545 | HTTPS FTP |
-Related structure data
Related structure data | 5mqfMC 3547C 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_3545.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.59 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_3545_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_3545_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human C* Spliceosome, masked refinement
+Supramolecule #1: Human C* Spliceosome, masked refinement
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #2: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #3: SNW domain-containing protein 1
+Macromolecule #4: Pleiotropic regulator 1
+Macromolecule #5: Pre-mRNA-processing factor 17
+Macromolecule #6: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #7: Pre-mRNA-processing factor 19
+Macromolecule #8: Pre-mRNA-splicing factor SPF27
+Macromolecule #9: Cell division cycle 5-like protein
+Macromolecule #10: Pre-mRNA-splicing factor SYF1
+Macromolecule #11: Pre-mRNA-splicing factor SYF2
+Macromolecule #12: Crooked neck-like protein 1
+Macromolecule #13: Pre-mRNA-splicing factor RBM22
+Macromolecule #14: Protein BUD31 homolog
+Macromolecule #15: Spliceosome-associated protein CWC15 homolog
+Macromolecule #16: Serine/arginine repetitive matrix protein 2
+Macromolecule #17: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #18: Intron-binding protein aquarius
+Macromolecule #19: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #20: U2 small nuclear ribonucleoprotein A'
+Macromolecule #21: U2 small nuclear ribonucleoprotein B''
+Macromolecule #22: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #23: Small nuclear ribonucleoprotein F
+Macromolecule #24: Small nuclear ribonucleoprotein E
+Macromolecule #25: Small nuclear ribonucleoprotein G
+Macromolecule #26: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #27: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #28: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #29: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #30: Eukaryotic initiation factor 4A-III
+Macromolecule #31: ATP-dependent RNA helicase DHX8
+Macromolecule #32: MINX pre-mRNA (intron)
+Macromolecule #33: Human gene for small nuclear RNA U2 (snRNA U2)
+Macromolecule #34: Homo sapiens U5 A small nuclear RNA
+Macromolecule #35: Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K |
-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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 2-17 / Average electron dose: 2.1 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Reconstruction from negatively stained particles |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136534 |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-5mqf: |