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- EMDB-8009: Combined Body and arm regions of the yeast spliceosomal U4/U6.U5 ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8009 | |||||||||
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Title | Combined Body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP by masked classification and refinement-Class 2 | |||||||||
![]() | Combined body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP from masked classification and refinement-class2 | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Nguyen THD / Galej WP / Bai X-C / Oubridge C / Newman AJ / Scheres SHW / Nagai K | |||||||||
![]() | ![]() 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 | ![]() | 195.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 46 KB 46 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 72.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.6 KB | Display | ![]() |
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Full document | ![]() | 77.7 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8006C ![]() 8007C ![]() 8008C ![]() 8010C ![]() 8011C ![]() 8012C ![]() 8013C ![]() 8014C ![]() 5gamC ![]() 5ganC ![]() 5gaoC ![]() 5gapC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Combined body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP from masked classification and refinement-class2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : tri-snRNP complex with 30 proteins and 3 snRNA
+Supramolecule #1: tri-snRNP complex with 30 proteins and 3 snRNA
+Macromolecule #1: U4 snRNA
+Macromolecule #2: U6 snRNA
+Macromolecule #21: U5 snRNA
+Macromolecule #3: Prp8
+Macromolecule #4: Prp4
+Macromolecule #5: Prp6
+Macromolecule #6: Dib1
+Macromolecule #7: Prp31
+Macromolecule #8: Prp3
+Macromolecule #9: Brr2
+Macromolecule #10: unknown proteins
+Macromolecule #11: SmB
+Macromolecule #12: U4 SmD1
+Macromolecule #13: SmD2
+Macromolecule #14: SmD3
+Macromolecule #15: SmE
+Macromolecule #16: SmF
+Macromolecule #17: SmG
+Macromolecule #18: Snu66
+Macromolecule #19: U5 SmE
+Macromolecule #20: U5 SmD1
+Macromolecule #22: Snu13
+Macromolecule #23: LSm2
+Macromolecule #24: LSm3
+Macromolecule #25: LSm4
+Macromolecule #26: LSm5
+Macromolecule #27: LSm6
+Macromolecule #28: LSm7
+Macromolecule #29: LSm8
+Macromolecule #30: Snu114
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
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 R 1.2/1.3 / 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
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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 / 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 |