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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8014 | |||||||||
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Title | Body region of the U4/U6.U5 tri-snRNP | |||||||||
![]() | Central region of the U4/U6.U5 tri-snRNP comprising Prp8, Dib1, Prp31, Prp6, Prp4, Prp3, Snu13, U4 snRNA and U6 snRNA | |||||||||
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Function / homology | ![]() spliceosomal conformational changes to generate catalytic conformation / snoRNA splicing / snoRNA guided rRNA 2'-O-methylation / positive regulation of primary miRNA processing / positive regulation of RNA binding / box C/D sno(s)RNA 3'-end processing / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U4/U6 snRNP / spliceosomal tri-snRNP complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Nguyen THD / Galej WP | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution. Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai / ![]() Abstract: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led ...U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre. | |||||||||
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 | ![]() | 196.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.5 KB 29.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.2 KB | Display | ![]() |
Images | ![]() | 233.6 KB | ||
Filedesc metadata | ![]() | 11.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gapMC ![]() 8006C ![]() 8007C ![]() 8008C ![]() 8009C ![]() 8010C ![]() 8011C ![]() 8012C ![]() 8013C ![]() 5gamC ![]() 5ganC ![]() 5gaoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Central region of the U4/U6.U5 tri-snRNP comprising Prp8, Dib1, Prp31, Prp6, Prp4, Prp3, Snu13, U4 snRNA and U6 snRNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Body region of the U4/U6.U5 tri-snRNP complex
+Supramolecule #1: Body region of the U4/U6.U5 tri-snRNP complex
+Macromolecule #1: U4 snRNA, 5' region, nucleotides 1-67
+Macromolecule #2: U6 snRNA
+Macromolecule #3: U5 snRNA
+Macromolecule #4: unknown protein
+Macromolecule #5: Pre-mRNA-splicing factor 8
+Macromolecule #6: U4/U6 small nuclear ribonucleoprotein PRP4
+Macromolecule #7: Pre-mRNA-splicing factor 6
+Macromolecule #8: Spliceosomal protein DIB1
+Macromolecule #9: Pre-mRNA-processing factor 31
+Macromolecule #10: U4/U6 small nuclear ribonucleoprotein PRP3
+Macromolecule #11: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #12: Pre-mRNA-splicing helicase BRR2
-Experimental details
-Structure determination
Method | ![]() |
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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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III Details: Grids were blotted at 4 deg C for 2 seconds before plunging.. |
Details | 3.5 microlitre of sample was applied to grid. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-5gap: |