+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8013 | |||||||||
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Title | Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP | |||||||||
Map data | Head Region of yeast spliceosomal U4/U6.U5 tri-snRNP. | |||||||||
Sample |
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Keywords | Transcription / pre-mRNA splicing / snRNP / GTPase / spliceosome | |||||||||
Function / homology | Function and homology information maturation of 5S rRNA / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex ...maturation of 5S rRNA / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / nucleic acid binding / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / Resolution: 4.2 Å | |||||||||
Authors | Nguyen THD / Galej WP | |||||||||
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_8013.map.gz | 195.9 MB | EMDB map data format | |
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Header (meta data) | emd-8013-v30.xml emd-8013.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8013_fsc.xml | 13.4 KB | Display | FSC data file |
Images | emd_8013.png | 179.8 KB | ||
Filedesc metadata | emd-8013.cif.gz | 8.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8013 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8013 | HTTPS FTP |
-Validation report
Summary document | emd_8013_validation.pdf.gz | 287 KB | Display | EMDB validaton report |
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Full document | emd_8013_full_validation.pdf.gz | 286.1 KB | Display | |
Data in XML | emd_8013_validation.xml.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8013 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8013 | HTTPS FTP |
-Related structure data
Related structure data | 5gaoMC 8006C 8007C 8008C 8009C 8010C 8011C 8012C 8014C 5gamC 5ganC 5gapC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8013.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Head Region of yeast spliceosomal U4/U6.U5 tri-snRNP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
+Supramolecule #1: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
+Macromolecule #1: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #2: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #3: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #4: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #5: Small nuclear ribonucleoprotein E
+Macromolecule #6: Small nuclear ribonucleoprotein F
+Macromolecule #7: Small nuclear ribonucleoprotein G
+Macromolecule #8: Snu66
+Macromolecule #9: Pre-mRNA-splicing helicase BRR2
+Macromolecule #11: Pre-mRNA-splicing factor 8
+Macromolecule #10: Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence
-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 / 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. |
-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: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: RECIPROCAL / Protocol: OTHER | ||||||
Output model | PDB-5gao: |