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Yorodumi- EMDB-6973: Cryo-EM structure of the yeast pre-B complex at an average resolu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6973 | ||||||||||||
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Title | Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region) | ||||||||||||
Map data | U1 snRNP region of the spliceosomal pre-B complex | ||||||||||||
Sample |
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Keywords | spliceosme / assemply / pre-B complex / U1 snRNP / Splicing | ||||||||||||
Function / homology | Function and homology information first spliceosomal transesterification activity / positive regulation of RNA binding / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex ...first spliceosomal transesterification activity / positive regulation of RNA binding / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / commitment complex / U2-type prespliceosome assembly / poly(U) RNA binding / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / U2 snRNP / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / U5 snRNP / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288c (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Bai R / Wan R | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Science / Year: 2018 Title: Structures of the fully assembled spliceosome before activation. Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Jianlin Lei / Yigong Shi / Abstract: The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 ...The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast 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_6973.map.gz | 226.8 MB | EMDB map data format | |
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Header (meta data) | emd-6973-v30.xml emd-6973.xml | 33 KB 33 KB | Display Display | EMDB header |
Images | emd_6973.png | 228.4 KB | ||
Filedesc metadata | emd-6973.cif.gz | 9.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6973 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6973 | HTTPS FTP |
-Related structure data
Related structure data | 5zwnMC 6972C 6974C 5zwmC 5zwoC C: citing same article (ref.) M: atomic model generated by this map |
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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_6973.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | U1 snRNP region of the spliceosomal pre-B complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.338 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 : Pre-B spliceosomal complex
+Supramolecule #1: Pre-B spliceosomal complex
+Macromolecule #1: pre-mRNA
+Macromolecule #2: U1 snRNA
+Macromolecule #3: U1 small nuclear ribonucleoprotein 70 kDa homolog
+Macromolecule #4: U1 small nuclear ribonucleoprotein C
+Macromolecule #5: U1 small nuclear ribonucleoprotein A
+Macromolecule #6: U1 small nuclear ribonucleoprotein component PRP42
+Macromolecule #7: Pre-mRNA-processing factor 39
+Macromolecule #8: Protein NAM8
+Macromolecule #9: 56 kDa U1 small nuclear ribonucleoprotein component
+Macromolecule #10: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #11: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #12: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #13: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #14: Small nuclear ribonucleoprotein E
+Macromolecule #15: Small nuclear ribonucleoprotein F
+Macromolecule #16: Small nuclear ribonucleoprotein G
+Macromolecule #17: U1 small nuclear ribonucleoprotein component SNU71
+Macromolecule #18: Protein LUC7
+Macromolecule #19: U1 snRNP
+Macromolecule #20: Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
+Macromolecule #21: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.9 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
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) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 500657 |