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Open data
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Basic information
Entry | Database: PDB / ID: 6y50 | ||||||
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Title | 5'domain of human 17S U2 snRNP | ||||||
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![]() | SPLICING / 17S U2 snRNP | ||||||
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 spliceosomal complex / U2-type precatalytic spliceosome ...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 spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / SAGA complex / U2 snRNP / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / 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 / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA processing / fibrillar center / nuclear matrix / mRNA splicing, via spliceosome / 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 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
![]() | Zhang, Z. / Will, C.L. / Bertram, K. / Luehrmann, R. / Stark, H. | ||||||
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![]() | ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 477.9 KB | Display | ![]() |
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PDB format | ![]() | 304.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 57.3 KB | Display | |
Data in CIF | ![]() | 95.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10688MC ![]() 6y53C ![]() 6y5qC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 4 molecules 9yqp
#1: Protein | Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SF3A3, SAP61 / Source: (natural) ![]() |
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#2: Protein | Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PHF5A / Source: (natural) ![]() |
#8: Protein | Mass: 85965.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HTATSF1 / Source: (natural) ![]() |
#9: Protein | Mass: 117576.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DDX46, KIAA0801 / Source: (natural) ![]() |
-Splicing factor 3B subunit ... , 4 types, 4 molecules x8vu
#3: Protein | Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SF3B5, SF3B10 / Source: (natural) ![]() |
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#4: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SF3B2, SAP145 / Source: (natural) ![]() |
#5: Protein | Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SF3B3, KIAA0017, SAP130 / Source: (natural) ![]() |
#6: Protein | Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SF3B1, SAP155 / Source: (natural) ![]() |
-RNA chain / Non-polymers , 2 types, 4 molecules 2![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#10: Chemical | #7: RNA chain | | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: human 17S U2 snRNP / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R3.5/1 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 0.01 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 72 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120070 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Space: REAL |