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Yorodumi- EMDB-8012: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRN... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8012 | |||||||||
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Title | The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom | |||||||||
Map data | The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP | |||||||||
Sample |
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Function / homology | Function and homology information Sm-like protein family complex / maturation of 5S rRNA / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / snoRNA guided rRNA 2'-O-methylation / positive regulation of RNA binding / box C/D sno(s)RNA 3'-end processing ...Sm-like protein family complex / maturation of 5S rRNA / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / snoRNA guided rRNA 2'-O-methylation / positive regulation of RNA binding / box C/D sno(s)RNA 3'-end processing / U4/U6 snRNP / generation of catalytic spliceosome for first transesterification step / deadenylation-dependent decapping of nuclear-transcribed mRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / splicing factor binding / P-body assembly / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / U4 snRNP / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U3 snoRNA binding / U1 snRNP / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / maturation of SSU-rRNA / U1 snRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / small-subunit processome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / metallopeptidase activity / cytosolic large ribosomal subunit / RNA helicase activity / nucleic acid binding / RNA helicase / mRNA binding / GTPase activity / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / Resolution: 3.7 Å | |||||||||
Authors | Nguyen THD / Galej WP / Bai XC / Oubridge C / Scheres SHW / Newman AJ / Nagai K | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nature / Year: 2015 Title: The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-chen Bai / Christos G Savva / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai / Abstract: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key ...U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8012.map.gz | 196.3 MB | EMDB map data format | |
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Header (meta data) | emd-8012-v30.xml emd-8012.xml | 48.4 KB 48.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8012_fsc.xml | 13.4 KB | Display | FSC data file |
Images | emd_8012.png | 54 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8012 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8012 | HTTPS FTP |
-Related structure data
Related structure data | 5ganMC 8006C 8007C 8008C 8009C 8010C 8011C 8013C 8014C 5gamC 5gaoC 5gapC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10073 (Title: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Angstrom (particle images) Data size: 75.2 Data #1: Aligned particle images of the yeast U4/U6.U5 tri-snRNP [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8012.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
+Supramolecule #1: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
+Macromolecule #1: U4 snRNA
+Macromolecule #2: U6 snRNA
+Macromolecule #19: U5 snRNA
+Macromolecule #3: Pre-mRNA-splicing factor 8
+Macromolecule #4: U4/U6 small nuclear ribonucleoprotein PRP4
+Macromolecule #5: Pre-mRNA-splicing factor 6
+Macromolecule #6: Spliceosomal protein DIB1
+Macromolecule #7: Pre-mRNA-processing factor 31
+Macromolecule #8: U4/U6 small nuclear ribonucleoprotein PRP3
+Macromolecule #9: Pre-mRNA-splicing helicase BRR2
+Macromolecule #10: Unknown protein
+Macromolecule #11: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #12: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #13: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #14: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #15: Small nuclear ribonucleoprotein E
+Macromolecule #16: Small nuclear ribonucleoprotein F
+Macromolecule #17: Small nuclear ribonucleoprotein G
+Macromolecule #18: Snu66
+Macromolecule #20: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #21: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #22: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #23: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #24: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #25: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #26: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #27: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #28: Pre-mRNA-splicing factor SNU114
+Macromolecule #29: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.9 / Component - Concentration: 1.0 mM / Component - Name: DTT |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 6.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER Details: Grids are made of holey carbon, carbon-coated and glow discharged in N-amylamine. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Quantum |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Number real images: 2477 / Average exposure time: 16.0 sec. / Average electron dose: 38.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL |
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Output model | PDB-5gan: |