[English] 日本語
![](img/lk-miru.gif)
- EMDB-3545: Cryo-EM structure of a human spliceosome activated for step 2 of ... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-3545 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex) | |||||||||
![]() | None | |||||||||
![]() |
| |||||||||
Function / homology | ![]() 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 / selenocysteine insertion sequence binding / regulation of translation at postsynapse, modulating synaptic transmission / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity ...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 / selenocysteine insertion sequence binding / regulation of translation at postsynapse, modulating synaptic transmission / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / negative regulation of excitatory postsynaptic potential / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / generation of catalytic spliceosome for first transesterification step / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of vitamin D receptor signaling pathway / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Deadenylation of mRNA / embryonic brain development / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / M-decay: degradation of maternal mRNAs by maternally stored factors / Prp19 complex / positive regulation of androgen receptor activity / poly(A) binding / snRNP binding / U1 snRNP binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / embryonic cranial skeleton morphogenesis / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / commitment complex / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / Notch binding / positive regulation of mRNA splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / RUNX3 regulates NOTCH signaling / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / exploration behavior / U1 snRNP / ubiquitin-ubiquitin ligase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / lipid biosynthetic process / positive regulation of neurogenesis / U2-type prespliceosome / cyclosporin A binding / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / SMAD binding / mitotic G2 DNA damage checkpoint signaling / associative learning / protein K63-linked ubiquitination / blastocyst development / protein peptidyl-prolyl isomerization / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / proteasomal protein catabolic process / U5 snRNP / positive regulation of G1/S transition of mitotic cell cycle Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||
![]() | Bertram K / Liu WT | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 164.8 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 57.8 KB 57.8 KB | Display Display | ![]() |
Images | ![]() | 46.8 KB | ||
Others | ![]() ![]() | 139.4 MB 139.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mqfMC ![]() 3547C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.59 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: #1
File | emd_3545_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_3545_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
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 |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 6.4 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 2-17 / Average electron dose: 2.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER / Details: Reconstruction from negatively stained particles |
---|---|
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 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: OTHER |
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | ![]() PDB-5mqf: |