+Open data
-Basic information
Entry | Database: PDB / ID: 6y53 | ||||||
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Title | human 17S U2 snRNP low resolution part | ||||||
Components |
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Keywords | SPLICING / 17S U2 snRNP | ||||||
Function / homology | Function and homology information U11/U12 snRNP / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 7-methylguanosine cap hypermethylation / chromatin-protein adaptor activity / B-WICH complex / histone pre-mRNA 3'end processing complex ...U11/U12 snRNP / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 7-methylguanosine cap hypermethylation / 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 / U2-type prespliceosome assembly / methylosome / protein methylation / splicing factor binding / U12-type spliceosomal complex / protein localization to site of double-strand break / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / poly-ADP-D-ribose modification-dependent protein binding / blastocyst formation / U4 snRNP / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / U2-type spliceosomal complex / : / telomerase RNA binding / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / commitment complex / U2-type catalytic step 2 spliceosome / U2 snRNP / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / spliceosomal complex assembly / U2-type prespliceosome / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / U5 snRNP / spliceosomal snRNP assembly / Cajal body / U2 snRNA binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway / viral genome replication / RNA splicing / regulation of DNA-templated transcription elongation / mRNA splicing, via spliceosome / double-strand break repair via homologous recombination / B-WICH complex positively regulates rRNA expression / positive regulation of neuron projection development / mRNA processing / fibrillar center / cytoplasmic ribonucleoprotein granule / 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 / regulation of transcription by RNA polymerase II / enzyme binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å | ||||||
Authors | Zhang, Z. / Will, C.L. / Bertram, K. / Luehrmann, R. / Stark, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nature / Year: 2020 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6y53.cif.gz | 467.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y53.ent.gz | 269.5 KB | Display | PDB format |
PDBx/mmJSON format | 6y53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/6y53 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/6y53 | HTTPS FTP |
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-Related structure data
Related structure data | 10689MC 6y50C 6y5qC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-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) Homo sapiens (human) / References: UniProt: P09661 |
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#2: Protein | Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579 |
-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) Homo sapiens (human) / References: UniProt: Q9Y3B4 |
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#8: Protein | Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427 |
#17: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435 |
#18: Protein | Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533 |
-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) Homo sapiens (human) / References: UniProt: Q7L014, RNA helicase |
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#9: Protein | Mass: 24642.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678 |
#16: Protein | Mass: 85965.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43719 |
-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) Homo sapiens (human) / References: UniProt: Q15459 |
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#6: Protein | Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428 |
#7: Protein | Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12874 |
-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) Homo sapiens (human) / References: UniProt: P62308 |
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#11: Protein | Mass: 13310.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314 |
#12: Protein | Mass: 13551.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316 |
#13: Protein | Mass: 13940.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318 |
#14: Protein | Mass: 10817.601 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304 |
#15: Protein | Mass: 9734.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306 |
-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) Homo sapiens (human) / References: GenBank: 36516 |
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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 |
-Sample preparation
Component | Name: human 17S U2 snRNP / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-Processing
EM software |
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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 |