+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19062 | |||||||||
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Title | BRR2 part of the human spliceosomal B complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | pre-mRNA splicing / pre-catalytic spliceosome / B complex / SPLICING | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Zhang Z / Kumar V / Dybkov O / Will CL / Urlaub H / Stark H / Luehrmann R | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: EMBO J / Year: 2024 Title: Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. Authors: Zhenwei Zhang / Vinay Kumar / Olexandr Dybkov / Cindy L Will / Henning Urlaub / Holger Stark / Reinhard Lührmann / Abstract: The B complex is a key intermediate stage of spliceosome assembly. To improve the structural resolution of monomeric, human spliceosomal B (hB) complexes and thereby generate a more comprehensive hB ...The B complex is a key intermediate stage of spliceosome assembly. To improve the structural resolution of monomeric, human spliceosomal B (hB) complexes and thereby generate a more comprehensive hB molecular model, we determined the cryo-EM structure of B complex dimers formed in the presence of ATP S. The enhanced resolution of these complexes allows a finer molecular dissection of how the 5' splice site (5'ss) is recognized in hB, and new insights into molecular interactions of FBP21, SNU23 and PRP38 with the U6/5'ss helix and with each other. It also reveals that SMU1 and RED are present as a heterotetrameric complex and are located at the interface of the B dimer protomers. We further show that MFAP1 and UBL5 form a 5' exon binding channel in hB, and elucidate the molecular contacts stabilizing the 5' exon at this stage. Our studies thus yield more accurate models of protein and RNA components of hB complexes. They further allow the localization of additional proteins and protein domains (such as SF3B6, BUD31 and TCERG1) whose position was not previously known, thereby uncovering new functions for B-specific and other hB proteins during pre-mRNA splicing. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19062.map.gz | 419.3 MB | EMDB map data format | |
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Header (meta data) | emd-19062-v30.xml emd-19062.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_19062.png | 57.3 KB | ||
Filedesc metadata | emd-19062.cif.gz | 3.7 KB | ||
Others | emd_19062_half_map_1.map.gz emd_19062_half_map_2.map.gz | 422 MB 420.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19062 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19062 | HTTPS FTP |
-Validation report
Summary document | emd_19062_validation.pdf.gz | 668.8 KB | Display | EMDB validaton report |
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Full document | emd_19062_full_validation.pdf.gz | 668.4 KB | Display | |
Data in XML | emd_19062_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_19062_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19062 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19062 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19062.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_19062_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19062_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human spliceosomal B complex
Entire | Name: human spliceosomal B complex |
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Components |
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-Supramolecule #1: human spliceosomal B complex
Supramolecule | Name: human spliceosomal B complex / type: complex / ID: 1 / Parent: 0 |
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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: 7.9 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: ab initio 3D |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 251564 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |