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- EMDB-8012: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRN... -
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Open data
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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 | |||||||||
![]() | The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP | |||||||||
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![]() | pre-mRNA splicing / snRNP / GTPase / U5 snRNA / Prp8 / spliceosome / U4/U6 snRNP / Brr2 / Snu114 / transcription | |||||||||
Function / homology | ![]() spliceosomal conformational changes to generate catalytic conformation / positive regulation of primary miRNA processing / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / maturation of 5S rRNA / snoRNA guided rRNA 2'-O-methylation / Lsm1-7-Pat1 complex / positive regulation of RNA binding / U6 snRNP / box C/D sno(s)RNA 3'-end processing ...spliceosomal conformational changes to generate catalytic conformation / positive regulation of primary miRNA processing / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / maturation of 5S rRNA / snoRNA guided rRNA 2'-O-methylation / Lsm1-7-Pat1 complex / positive regulation of RNA binding / U6 snRNP / box C/D sno(s)RNA 3'-end processing / deadenylation-dependent decapping of nuclear-transcribed mRNA / generation of catalytic spliceosome for first transesterification step / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / P-body assembly / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U3 snoRNA binding / U1 snRNP / tRNA processing / U2-type prespliceosome / positive regulation of miRNA metabolic process / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / mRNA 5'-splice site recognition / nuclear-transcribed mRNA catabolic process / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / cellular response to glucose starvation / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / maturation of LSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spliceosomal complex / P-body / mRNA splicing, via spliceosome / rRNA processing / metallopeptidase activity / cytosolic large ribosomal subunit / nucleic acid binding / RNA helicase activity / RNA helicase / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / Resolution: 3.7 Å | |||||||||
![]() | Nguyen THD / Galej WP | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 196.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 50.5 KB 50.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 54 KB | ||
Filedesc metadata | ![]() | 13.7 KB | ||
Archive directory | ![]() ![]() | 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 ( |
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Similar structure data | |
EM raw data | ![]() Data size: 75.2 Data #1: Aligned particle images of the yeast U4/U6.U5 tri-snRNP [picked particles - multiframe - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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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
![]() | single particle reconstruction |
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Aggregation state | particle |
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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Pretreatment - Atmosphere: OTHER Details: Grids are made of holey carbon, carbon-coated and glow discharged in N-amylamine. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL |
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Output model | ![]() PDB-5gan: |