+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34841 | |||||||||
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Title | The cryo-EM structure of human pre-17S U2 snRNP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DDX42 / U2 snRNP / spliceosome / SPLICING | |||||||||
Function / homology | Function and homology information 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 / 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 / SAGA complex / positive regulation of transcription by RNA polymerase III / U1 snRNP / Cajal body / 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 / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / 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 / negative regulation of protein catabolic process / stem cell differentiation / spliceosomal complex / double-strand break repair via homologous recombination / B-WICH complex positively regulates rRNA expression / fibrillar center / positive regulation of neuron projection development / nuclear matrix / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / mRNA processing / protein localization / site of double-strand break / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / spermatogenesis / regulation of apoptotic process / RNA helicase activity / chromatin remodeling / nuclear body / RNA helicase / nuclear speck / mRNA binding / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Zhang X / Zhan X / Shi Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. Authors: Fenghua Yang / Tong Bian / Xiechao Zhan / Zhe Chen / Zhihan Xing / Nicolas A Larsen / Xiaofeng Zhang / Yigong Shi / Abstract: Three RNA helicases - DDX42, DDX46 and DHX15 - are found to be associated with human U2 snRNP, but their roles and mechanisms in U2 snRNP and spliceosome assembly are insufficiently understood. Here ...Three RNA helicases - DDX42, DDX46 and DHX15 - are found to be associated with human U2 snRNP, but their roles and mechanisms in U2 snRNP and spliceosome assembly are insufficiently understood. Here we report the cryo-electron microscopy (cryo-EM) structures of the DDX42-SF3b complex and a putative assembly precursor of 17S U2 snRNP that contains DDX42 (DDX42-U2 complex). DDX42 is anchored on SF3B1 through N-terminal sequences, with its N-plug occupying the RNA path of SF3B1. The binding mode of DDX42 to SF3B1 is in striking analogy to that of DDX46. In the DDX42-U2 complex, the N-terminus of DDX42 remains anchored on SF3B1, but the helicase domain has been displaced by U2 snRNA and TAT-SF1. Through in vitro assays, we show DDX42 and DDX46 are mutually exclusive in terms of binding to SF3b. Cancer-driving mutations of SF3B1 target the residues in the RNA path that directly interact with DDX42 and DDX46. These findings reveal the distinct roles of DDX42 and DDX46 in assembly of 17S U2 snRNP and provide insights into the mechanisms of SF3B1 cancer mutations. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34841.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-34841-v30.xml emd-34841.xml | 39.2 KB 39.2 KB | Display Display | EMDB header |
Images | emd_34841.png | 94 KB | ||
Others | emd_34841_half_map_1.map.gz emd_34841_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34841 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34841 | HTTPS FTP |
-Validation report
Summary document | emd_34841_validation.pdf.gz | 811.8 KB | Display | EMDB validaton report |
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Full document | emd_34841_full_validation.pdf.gz | 811.4 KB | Display | |
Data in XML | emd_34841_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_34841_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34841 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34841 | HTTPS FTP |
-Related structure data
Related structure data | 8hk1MC 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_34841.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Half map: #1
File | emd_34841_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34841_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The human pre-17S U2 snRNP
+Supramolecule #1: The human pre-17S 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: ATP-dependent RNA helicase DDX42
+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
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 430443 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |