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Yorodumi- EMDB-3547: Cryo-EM structure of a human spliceosome activated for step 2 of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3547 | |||||||||
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Title | Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.4 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_3547.map.gz | 162.1 MB | EMDB map data format | |
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Header (meta data) | emd-3547-v30.xml emd-3547.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
Images | emd_3547.png | 53.5 KB | ||
Others | emd_3547_half_map_1.map.gz emd_3547_half_map_2.map.gz | 139.5 MB 139.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3547 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3547 | HTTPS FTP |
-Validation report
Summary document | emd_3547_validation.pdf.gz | 342.3 KB | Display | EMDB validaton report |
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Full document | emd_3547_full_validation.pdf.gz | 341.5 KB | Display | |
Data in XML | emd_3547_validation.xml.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3547 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3547 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3547.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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_3547_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_3547_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human C* Spliceosome, unmasked refinement
Entire | Name: Human C* Spliceosome, unmasked refinement |
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Components |
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-Supramolecule #1: Human C* Spliceosome, unmasked refinement
Supramolecule | Name: Human C* Spliceosome, unmasked refinement / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#41 |
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Source (natural) | Organism: Homo sapiens (human) |
-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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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: FIELD EMISSION GUN |
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 |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.4 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 |
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