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Open data
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Basic information
Entry | Database: PDB / ID: 6y53 | ||||||
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Title | human 17S U2 snRNP low resolution part | ||||||
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![]() | SPLICING / 17S U2 snRNP | ||||||
Function / homology | ![]() U11/U12 snRNP / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / chromatin-protein adaptor activity / B-WICH complex / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs ...U11/U12 snRNP / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / chromatin-protein adaptor activity / B-WICH complex / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / splicing factor binding / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / protein localization to site of double-strand break / poly-ADP-D-ribose modification-dependent protein binding / snRNP binding / U1 snRNP binding / blastocyst formation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / positive regulation of mRNA splicing, via spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / double-strand break repair via homologous recombination / B-WICH complex positively regulates rRNA expression / fibrillar center / positive regulation of neuron projection development / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / mRNA processing / site of double-strand break / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / spermatogenesis / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 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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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 474.1 KB | Display | ![]() |
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PDB format | ![]() | 260.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10689MC ![]() 6y50C ![]() 6y5qC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules ab
#1: Protein | Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Splicing factor 3B subunit ... , 4 types, 4 molecules zo8u
#3: Protein | Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#8: Protein | Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#18: Protein | Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 3 types, 3 molecules pmq
#4: Protein | Mass: 117576.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#9: Protein | Mass: 24642.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#16: Protein | Mass: 85965.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Splicing factor 3A subunit ... , 3 types, 3 molecules 679
#5: Protein | Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#6: Protein | Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Small nuclear ribonucleoprotein ... , 6 types, 6 molecules knhlji
#10: Protein | Mass: 8508.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#11: Protein | Mass: 13310.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 13551.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 13940.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 10817.601 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 9734.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 1 types, 1 molecules 2
#19: RNA chain | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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: all / 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 | ||||||||||||||||||||
3D reconstruction | Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120070 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Space: REAL |