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Yorodumi- EMDB-9524: Cryo-EM structure of the activated spliceosome (Bact complex) at ... -
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-Basic information
Entry | Database: EMDB / ID: EMD-9524 | |||||||||
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Title | Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution | |||||||||
Map data | Cryo-EM map of Bact spliceosome at 3.5-angstrom resolution | |||||||||
Sample |
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Function / homology | Function and homology information maintenance of RNA location / U2-type post-mRNA release spliceosomal complex / RES complex / mRNA branch site recognition / snoRNA splicing / cellular bud site selection / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) ...maintenance of RNA location / U2-type post-mRNA release spliceosomal complex / RES complex / mRNA branch site recognition / snoRNA splicing / cellular bud site selection / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / Prp19 complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / ATP-dependent activity, acting on RNA / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / Dual incision in TC-NER / DNA replication origin binding / generation of catalytic spliceosome for second transesterification step / protein K63-linked ubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / DNA replication initiation / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / mRNA export from nucleus / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / positive regulation of cell cycle / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / nuclear periphery / positive regulation of RNA splicing / RNA splicing / peptidylprolyl isomerase / helicase activity / peptidyl-prolyl cis-trans isomerase activity / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / mRNA processing / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / RNA helicase activity / nucleic acid binding / RNA helicase / response to xenobiotic stimulus / cell cycle / DNA repair / mRNA binding / GTPase activity / chromatin binding / chromatin / GTP binding / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) / Baker's yeast (brewer's yeast) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Yan C / Wan R / Bai R / Huang G / Shi Y | |||||||||
Citation | Journal: Science / Year: 2016 Title: Structure of a yeast activated spliceosome at 3.5 Å resolution. Authors: Chuangye Yan / Ruixue Wan / Rui Bai / Gaoxingyu Huang / Yigong Shi / Abstract: Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome ...Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3.52 angstroms. The final refined model contains U2 and U5 small nuclear ribonucleoprotein particles (snRNPs), U6 small nuclear RNA (snRNA), nineteen complex (NTC), NTC-related (NTR) protein, and a 71-nucleotide pre-mRNA molecule, which amount to 13,505 amino acids from 38 proteins and a combined molecular mass of about 1.6 megadaltons. The 5' exon is anchored by loop I of U5 snRNA, whereas the 5' splice site (5'SS) and the branch-point sequence (BPS) of the intron are specifically recognized by U6 and U2 snRNA, respectively. Except for coordination of the catalytic metal ions, the RNA elements at the catalytic cavity of Prp8 are mostly primed for catalysis. The catalytic latency is maintained by the SF3b complex, which encircles the BPS, and the splicing factors Cwc24 and Prp11, which shield the 5' exon-5'SS junction. This structure, together with those determined earlier, outlines a molecular framework for the pre-mRNA splicing reaction. | |||||||||
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_9524.map.gz | 228.9 MB | EMDB map data format | |
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Header (meta data) | emd-9524-v30.xml emd-9524.xml | 69.2 KB 69.2 KB | Display Display | EMDB header |
Images | emd_9524.png | 234.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9524 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9524 | HTTPS FTP |
-Related structure data
Related structure data | 5gm6MC 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_9524.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of Bact spliceosome at 3.5-angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.306 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 : Bact spliceosomal complex
+Supramolecule #1: Bact spliceosomal complex
+Macromolecule #1: Pre-mRNA-splicing factor 8
+Macromolecule #2: Pre-mRNA-splicing helicase BRR2
+Macromolecule #3: Pre-mRNA-splicing factor SNU114
+Macromolecule #6: Pre-mRNA-splicing factor RSE1
+Macromolecule #7: Cold sensitive U2 snRNA suppressor 1
+Macromolecule #8: Pre-mRNA-splicing factor PRP11
+Macromolecule #9: Pre-mRNA-splicing factor RDS3
+Macromolecule #10: RDS3 complex subunit 10
+Macromolecule #14: Pre-mRNA-splicing factor PRP46
+Macromolecule #15: Pre-mRNA-processing protein 45
+Macromolecule #16: Pre-mRNA-splicing factor SLT11
+Macromolecule #17: Pre-mRNA-splicing factor CWC2
+Macromolecule #18: Pre-mRNA-splicing factor CWC15
+Macromolecule #19: Pre-mRNA-splicing factor BUD31
+Macromolecule #20: Pre-mRNA leakage protein 1
+Macromolecule #21: U2 snRNP component IST3
+Macromolecule #22: Pre-mRNA-splicing factor CWC26
+Macromolecule #23: Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
+Macromolecule #24: Pre-mRNA-splicing factor CWC22
+Macromolecule #25: Pre-mRNA-splicing factor CWC24
+Macromolecule #26: Peptidyl-prolyl isomerase CWC27
+Macromolecule #27: Pre-mRNA-splicing factor CEF1
+Macromolecule #28: U2 snRNP component HSH155
+Macromolecule #29: Pre-mRNA-splicing factor CLF1
+Macromolecule #30: Pre-mRNA-splicing factor CWC21
+Macromolecule #31: Pre-mRNA-splicing factor SYF1
+Macromolecule #32: Protein HSH49
+Macromolecule #33: Pre-mRNA-splicing factor SYF2
+Macromolecule #34: Pre-mRNA-processing factor 19
+Macromolecule #35: Pre-mRNA-splicing factor SNT309
+Macromolecule #36: Pre-mRNA-processing factor 17
+Macromolecule #37: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #38: Small nuclear ribonucleoprotein E
+Macromolecule #39: Small nuclear ribonucleoprotein F
+Macromolecule #40: Small nuclear ribonucleoprotein G
+Macromolecule #41: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #42: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #43: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #4: Saccharomyces cerevisiae strain CDRDR_sf_H chromosome VII sequence
+Macromolecule #5: Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence
+Macromolecule #11: U2 snRNA
+Macromolecule #12: Pre-mRNA
+Macromolecule #13: Pre-mRNA
+Macromolecule #44: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #45: MAGNESIUM ION
+Macromolecule #46: ZINC ION
+Macromolecule #47: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Details: CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA) |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Scanner: OTHER / Average electron dose: 4.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
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Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77312 |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-5gm6: |