+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43753 | |||||||||
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Title | Yeast U1 snRNP with humanized U1C Zinc-Finger domain | |||||||||
Map data | ||||||||||
Sample |
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Keywords | U1snRNP / U1C humanization / SPLICING | |||||||||
Function / homology | Function and homology information positive regulation of RNA binding / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / positive regulation of mRNA splicing, via spliceosome ...positive regulation of RNA binding / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / positive regulation of mRNA splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / poly(U) RNA binding / U4 snRNP / U2 snRNP / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / U5 snRNP / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / mRNA binding / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
Authors | Shi SS / Kuang ZL / Zhao R | |||||||||
Funding support | United States, 2 items
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Citation | Journal: RNA / Year: 2024 Title: Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. Authors: Subbaiah Chalivendra / Shasha Shi / Xueni Li / Zhiling Kuang / Joseph Giovinazzo / Lingdi Zhang / John Rossi / Jingxin Wang / Anthony Saviola / Robb Welty / Shiheng Liu / Katherine Vaeth / Z ...Authors: Subbaiah Chalivendra / Shasha Shi / Xueni Li / Zhiling Kuang / Joseph Giovinazzo / Lingdi Zhang / John Rossi / Jingxin Wang / Anthony Saviola / Robb Welty / Shiheng Liu / Katherine Vaeth / Z Hong Zhou / Kirk Hansen / J Matthew Taliaferro / Rui Zhao / Abstract: The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized ...The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5' ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in a cold-sensitive growth phenotype and moderate splicing defects. We next added an auxin-inducible degron to yLuc7 protein (to mimic the lack of Luc7Ls in human U1 snRNP) and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondrial function in yeast. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43753.map.gz | 945.1 MB | EMDB map data format | |
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Header (meta data) | emd-43753-v30.xml emd-43753.xml | 38.2 KB 38.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43753_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_43753.png | 101.8 KB | ||
Filedesc metadata | emd-43753.cif.gz | 10 KB | ||
Others | emd_43753_half_map_1.map.gz emd_43753_half_map_2.map.gz | 927.9 MB 927.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43753 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43753 | HTTPS FTP |
-Related structure data
Related structure data | 8w2oMC 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_43753.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_43753_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43753_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : U1snRNP
+Supramolecule #1: U1snRNP
+Macromolecule #1: U1 small nuclear ribonucleoprotein 70 kDa homolog
+Macromolecule #2: U1 small nuclear ribonucleoprotein C
+Macromolecule #3: U1 small nuclear ribonucleoprotein A
+Macromolecule #4: U1 small nuclear ribonucleoprotein component PRP42
+Macromolecule #5: Pre-mRNA-processing factor 39
+Macromolecule #6: Protein NAM8
+Macromolecule #7: 56 kDa U1 small nuclear ribonucleoprotein component
+Macromolecule #8: U1 small nuclear ribonucleoprotein component SNU71
+Macromolecule #9: Protein LUC7
+Macromolecule #10: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #11: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #12: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #13: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #14: Small nuclear ribonucleoprotein E
+Macromolecule #15: Small nuclear ribonucleoprotein F
+Macromolecule #16: Small nuclear ribonucleoprotein G
+Macromolecule #17: ACT1 pre-mRNA
+Macromolecule #18: U1 snRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | ||||||||||||
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Buffer | pH: 7.9 Component:
Details: 20 mM Hepes, pH7.9, 120 mM KCl, 2 mM EGTA | ||||||||||||
Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: The grids were obtained with the chamber at 100% humidity, 2.5 s blotting time, -6 blotting force and 15 s wait time and flash-frozen into liquid ethane with a Vitrobot Mark IV (Thermo Fisher Scientific). | ||||||||||||
Details | This sample is monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |