+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-10688 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 5'domain of human 17S U2 snRNP | |||||||||
![]() | 5'domain of human 17S U2 snRNP | |||||||||
![]() |
| |||||||||
![]() | 17S U2 snRNP / SPLICING | |||||||||
Function / homology | ![]() U11/U12 snRNP / chromatin-protein adaptor activity / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / protein localization to site of double-strand break / poly-ADP-D-ribose modification-dependent protein binding / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type spliceosomal complex ...U11/U12 snRNP / chromatin-protein adaptor activity / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / protein localization to site of double-strand break / poly-ADP-D-ribose modification-dependent protein binding / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / SAGA complex / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / U2 snRNA binding / regulation of DNA repair / Cajal body / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / double-strand break repair via homologous recombination / negative regulation of protein catabolic process / B-WICH complex positively regulates rRNA expression / fibrillar center / nuclear matrix / mRNA splicing, via spliceosome / mRNA processing / site of double-strand break / RNA helicase activity / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Zhang Z / Will CL | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Molecular architecture of the human 17S U2 snRNP. Authors: Zhenwei Zhang / Cindy L Will / Karl Bertram / Olexandr Dybkov / Klaus Hartmuth / Dmitry E Agafonov / Romina Hofele / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark / ![]() ![]() Abstract: The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing. Stable addition of ...The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing. Stable addition of U2 during early spliceosome formation requires the DEAD-box ATPase PRP5. Yeast U2 small nuclear RNA (snRNA) nucleotides that form base pairs with the branch site are initially sequestered in a branchpoint-interacting stem-loop (BSL), but whether the human U2 snRNA folds in a similar manner is unknown. The U2 SF3B1 protein, a common mutational target in haematopoietic cancers, contains a HEAT domain (SF3B1) with an open conformation in isolated SF3b, but a closed conformation in spliceosomes, which is required for stable interaction between U2 and the branch site. Here we report a 3D cryo-electron microscopy structure of the human 17S U2 snRNP at a core resolution of 4.1 Å and combine it with protein crosslinking data to determine the molecular architecture of this snRNP. Our structure reveals that SF3B1 interacts with PRP5 and TAT-SF1, and maintains its open conformation in U2 snRNP, and that U2 snRNA forms a BSL that is sandwiched between PRP5, TAT-SF1 and SF3B1. Thus, substantial remodelling of the BSL and displacement of BSL-interacting proteins must occur to allow formation of the U2-branch-site helix. Our studies provide a structural explanation of why TAT-SF1 must be displaced before the stable addition of U2 to the spliceosome, and identify RNP rearrangements facilitated by PRP5 that are required for stable interaction between U2 and the branch site. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 95.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 23.7 KB 23.7 KB | Display Display | ![]() |
Images | ![]() | 56.7 KB | ||
Filedesc metadata | ![]() | 9.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y50MC ![]() 6y53C ![]() 6y5qC 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 | 5'domain of human 17S U2 snRNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : human 17S U2 snRNP
+Supramolecule #1: human 17S U2 snRNP
+Macromolecule #1: Splicing factor 3A subunit 3
+Macromolecule #2: PHD finger-like domain-containing protein 5A
+Macromolecule #3: Splicing factor 3B subunit 5
+Macromolecule #4: Splicing factor 3B subunit 2
+Macromolecule #5: Splicing factor 3B subunit 3
+Macromolecule #6: Splicing factor 3B subunit 1
+Macromolecule #8: HIV Tat-specific factor 1
+Macromolecule #9: Probable ATP-dependent RNA helicase DDX46
+Macromolecule #7: U2 snRNA
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.9 |
---|---|
Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 72.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 120070 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | ![]() PDB-6y50: |