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- EMDB-6974: Cryo-EM structure of the yeast B complex at average resolution of... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6974 | ||||||||||||
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Title | Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom | ||||||||||||
![]() | cryo-EM structure of the spliceosomal B complex | ||||||||||||
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Function / homology | ![]() maintenance of RNA location / RES complex / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / protein serine/threonine phosphatase inhibitor activity / snoRNA splicing / negative regulation of protein dephosphorylation / maturation of 5S rRNA / snoRNA guided rRNA 2'-O-methylation / Lsm1-7-Pat1 complex ...maintenance of RNA location / RES complex / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / protein serine/threonine phosphatase inhibitor activity / snoRNA splicing / negative regulation of protein dephosphorylation / maturation of 5S rRNA / snoRNA guided rRNA 2'-O-methylation / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA 3'-end processing / positive regulation of RNA binding / generation of catalytic spliceosome for first transesterification step / deadenylation-dependent decapping of nuclear-transcribed mRNA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Shi Y / Bai R | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 227.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 69.3 KB 69.3 KB | Display Display | ![]() |
Images | ![]() | 170.7 KB | ||
Filedesc metadata | ![]() | 18.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zwoMC ![]() 6972C ![]() 6973C ![]() 5zwmC ![]() 5zwnC 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
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Annotation | cryo-EM structure of the spliceosomal 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
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Sample components
+Entire : yeast fully assembled spliceosomal B complex before activation
+Supramolecule #1: yeast fully assembled spliceosomal B complex before activation
+Macromolecule #1: Pre-mRNA-splicing factor 8
+Macromolecule #2: U4/U6 small nuclear ribonucleoprotein PRP4
+Macromolecule #3: Pre-mRNA-processing factor 31
+Macromolecule #4: Pre-mRNA-splicing factor 6
+Macromolecule #5: U4/U6 small nuclear ribonucleoprotein PRP3
+Macromolecule #6: Spliceosomal protein DIB1
+Macromolecule #7: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #8: Pre-mRNA-splicing factor SNU114
+Macromolecule #9: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #10: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #11: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #12: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #13: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #14: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #15: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #18: 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #20: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #21: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #22: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #23: Small nuclear ribonucleoprotein E
+Macromolecule #24: Small nuclear ribonucleoprotein F
+Macromolecule #25: Small nuclear ribonucleoprotein G
+Macromolecule #27: Pre-mRNA-splicing helicase BRR2
+Macromolecule #29: U2 snRNP component HSH155
+Macromolecule #30: Cold sensitive U2 snRNA suppressor 1
+Macromolecule #31: Pre-mRNA-splicing factor RSE1
+Macromolecule #32: Protein HSH49
+Macromolecule #33: Pre-mRNA-splicing factor RDS3
+Macromolecule #34: RDS3 complex subunit 10
+Macromolecule #35: U2 snRNP component IST3
+Macromolecule #36: Pre-mRNA-splicing factor CWC26
+Macromolecule #37: Pre-mRNA leakage protein 1
+Macromolecule #39: U2 small nuclear ribonucleoprotein A'
+Macromolecule #40: U2 small nuclear ribonucleoprotein B''
+Macromolecule #41: Pre-mRNA-splicing factor PRP9
+Macromolecule #42: Pre-mRNA-splicing factor PRP21
+Macromolecule #43: Pre-mRNA-splicing factor PRP11
+Macromolecule #44: 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component
+Macromolecule #45: Pre-mRNA-splicing factor 38
+Macromolecule #46: Pre-mRNA-splicing factor SPP381
+Macromolecule #16: U6 snRNA
+Macromolecule #17: U5 snRNA
+Macromolecule #26: U4 snRNA
+Macromolecule #28: Pre-mRNA
+Macromolecule #38: U2 snRNA
+Macromolecule #47: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #48: MAGNESIUM ION
-Experimental details
-Structure determination
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Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.9 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 342588 |