+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31334 | |||||||||
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Title | The cryo-EM map of the human 17S U2 snRNP core region | |||||||||
Map data | The EM map of U2 snRNP | |||||||||
Sample |
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Keywords | U2 snRNP / PRP5 / SF3B1 / Splicing | |||||||||
Function / homology | Function and homology information U11/U12 snRNP / poly-ADP-D-ribose modification-dependent protein binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / chromatin-protein adaptor activity / SLBP independent Processing of Histone Pre-mRNAs ...U11/U12 snRNP / poly-ADP-D-ribose modification-dependent protein binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / chromatin-protein adaptor activity / 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 / U1 snRNP binding / pICln-Sm protein complex / snRNP binding / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / SAGA complex / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / 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 / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / regulation of RNA splicing / mRNA 3'-splice site recognition / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / 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 / fibrillar center / mRNA splicing, via spliceosome / positive regulation of neuron projection development / nuclear matrix / cytoplasmic ribonucleoprotein granule / mRNA processing / site of double-strand break / snRNP Assembly / spermatogenesis / SARS-CoV-2 modulates host translation machinery / nucleic acid binding / RNA helicase activity / nuclear body / hydrolase activity / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Zhang X / Zhan X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural insights into branch site proofreading by human spliceosome. Authors: Xiaofeng Zhang / Xiechao Zhan / Tong Bian / Fenghua Yang / Pan Li / Yichen Lu / Zhihan Xing / Rongyan Fan / Qiangfeng Cliff Zhang / Yigong Shi / Abstract: Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the ...Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31334.map.gz | 116.7 MB | EMDB map data format | |
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Header (meta data) | emd-31334-v30.xml emd-31334.xml | 36.4 KB 36.4 KB | Display Display | EMDB header |
Images | emd_31334.png | 35.5 KB | ||
Filedesc metadata | emd-31334.cif.gz | 12.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31334 | HTTPS FTP |
-Validation report
Summary document | emd_31334_validation.pdf.gz | 547.7 KB | Display | EMDB validaton report |
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Full document | emd_31334_full_validation.pdf.gz | 547.3 KB | Display | |
Data in XML | emd_31334_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_31334_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31334 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31334 | HTTPS FTP |
-Related structure data
Related structure data | 7evoMC 7vpxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31334.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The EM map of U2 snRNP | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : The human U2 snRNP
+Supramolecule #1: The human U2 snRNP
+Macromolecule #1: U2 snRNA
+Macromolecule #2: Splicing factor 3B subunit 1
+Macromolecule #3: Splicing factor 3B subunit 2
+Macromolecule #4: Splicing factor 3B subunit 3
+Macromolecule #5: Splicing factor 3B subunit 4
+Macromolecule #6: Splicing factor 3B subunit 5
+Macromolecule #7: PHD finger-like domain-containing protein 5A
+Macromolecule #8: Splicing factor 3A subunit 1
+Macromolecule #9: Splicing factor 3A subunit 2
+Macromolecule #10: Splicing factor 3A subunit 3
+Macromolecule #11: HIV Tat-specific factor 1
+Macromolecule #12: RNA helicase
+Macromolecule #13: U2 small nuclear ribonucleoprotein A'
+Macromolecule #14: U2 small nuclear ribonucleoprotein B''
+Macromolecule #15: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #16: Small nuclear ribonucleoprotein F
+Macromolecule #17: Small nuclear ribonucleoprotein E
+Macromolecule #18: Small nuclear ribonucleoprotein G
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #20: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #21: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #22: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~...
+Macromolecule #23: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.9 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 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 / Details: Initial model from CryoSparc |
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Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 485418 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |