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- EMDB-6413: Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6413 | |||||||||
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Title | Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution | |||||||||
![]() | Reconstruction of spliceosome | |||||||||
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Function / homology | ![]() : / : / : / : / protein modification by small protein conjugation or removal / regulation of siRNA-mediated facultative heterochromatin formation / Transport of Mature mRNA derived from an Intron-Containing Transcript / second spliceosomal transesterification activity / : / Dual incision in TC-NER ...: / : / : / : / protein modification by small protein conjugation or removal / regulation of siRNA-mediated facultative heterochromatin formation / Transport of Mature mRNA derived from an Intron-Containing Transcript / second spliceosomal transesterification activity / : / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / spliceosomal conformational changes to generate catalytic conformation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U12-type spliceosomal complex / Prp19 complex / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / Cul4-RING E3 ubiquitin ligase complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / protein folding / nuclear envelope / cysteine-type deubiquitinase activity / ribonucleoprotein complex / cell cycle / DNA repair / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Yan C / Hang J / Wan R / Huang M / Wong C / Shi Y | |||||||||
![]() | ![]() Title: Structure of a yeast spliceosome at 3.6-angstrom resolution. Authors: Chuangye Yan / Jing Hang / Ruixue Wan / Min Huang / Catherine C L Wong / Yigong Shi / ![]() Abstract: Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins ...Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing. | |||||||||
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 | ![]() | 166.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.4 KB 9.4 KB | Display Display | ![]() |
Images | ![]() ![]() | 59.3 KB 4.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 391.9 KB | Display | ![]() |
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Full document | ![]() | 391.4 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jb9MC ![]() 6414C ![]() 6415C ![]() 6416C ![]() 6417C ![]() 6418C ![]() 6419C ![]() 6420C ![]() 6421C C: citing same article ( M: atomic model generated by this map |
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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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of spliceosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 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 : spliceosome
Entire | Name: spliceosome |
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Components |
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-Supramolecule #1000: spliceosome
Supramolecule | Name: spliceosome / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: Spliceosome
Macromolecule | Name: Spliceosome / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 8 Details: 75mM NaCl, 10mM Tris-HCL,1mM Mg(OAc)2,1mM imidazole, 0.01% NP40, 1mM TCEP, 2mM EGTA |
Grid | Details: carbon coated grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2.5 seconds before plunging |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Mar 29, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 2246 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 112795 |
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