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- PDB-6j6g: Cryo-EM structure of the yeast B*-a2 complex at an average resolu... -
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Basic information
Entry | Database: PDB / ID: 6j6g | ||||||||||||
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Title | Cryo-EM structure of the yeast B*-a2 complex at an average resolution of 3.2 angstrom | ||||||||||||
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![]() | SPLICING / spliceosme / B* complex / branching / snRNP / U snRNA | ||||||||||||
Function / homology | ![]() post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / cellular bud site selection / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) ...post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / cellular bud site selection / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / Prp19 complex / snRNP binding / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / Formation of TC-NER Pre-Incision Complex / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication origin binding / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / Dual incision in TC-NER / DNA replication initiation / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / positive regulation of cell cycle / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / nuclear periphery / positive regulation of RNA splicing / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / DNA repair / chromatin binding / GTPase activity / mRNA binding / chromatin / GTP binding / mitochondrion / DNA binding / RNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Wan, R. / Bai, R. / Yan, C. / Lei, J. / Shi, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Authors: Ruixue Wan / Rui Bai / Chuangye Yan / Jianlin Lei / Yigong Shi / ![]() Abstract: Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B) is pivotal for understanding the branching reaction. In this study, we ...Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B) is pivotal for understanding the branching reaction. In this study, we assembled the B complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0686MC ![]() 0684C ![]() 0685C ![]() 0687C ![]() 0691C ![]() 0692C ![]() 6j6hC ![]() 6j6nC ![]() 6j6qC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Pre-mRNA-splicing factor ... , 15 types, 15 molecules ACJOQRSTZcdIHvt
#1: Protein | Mass: 279867.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P33334 |
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#2: Protein | Mass: 114174.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P36048 |
#3: Protein | Mass: 15793.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q03375 |
#4: Protein | Mass: 50771.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12417 |
#6: Protein | Mass: 40988.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38241 |
#7: Protein | Mass: 38486.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12046 |
#8: Protein | Mass: 19975.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q03772 |
#9: Protein | Mass: 18484.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P25337 |
#10: Protein | Mass: 67386.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53333 |
#11: Protein | Mass: 67837.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q03654 |
#12: Protein | Mass: 82555.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12309 |
#13: Protein | Mass: 24850.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53277 |
#15: Protein | Mass: 28073.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P21374 |
#20: Protein | Mass: 100344.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q04048 |
#23: Protein | Mass: 20741.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06091 |
-Protein , 2 types, 3 molecules Pks
#5: Protein | Mass: 42548.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P28004 |
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#29: Protein | Mass: 22426.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40018 |
-Pre-mRNA-processing factor ... , 2 types, 5 molecules nrpqo
#14: Protein | Mass: 52208.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40968 |
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#31: Protein | Mass: 56629.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P32523, RING-type E3 ubiquitin transferase |
-RNA chain , 4 types, 4 molecules BDEL
#16: RNA chain | Mass: 217099.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#17: RNA chain | Mass: 68643.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: RNA chain | Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: RNA chain | Mass: 376267.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules ab
#21: Protein | Mass: 12850.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40567 |
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#22: Protein | Mass: 27232.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q08963 |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules uimzjxhwgely
#24: Protein | Mass: 10385.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12330 #25: Protein | Mass: 16296.798 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02260 #26: Protein | Mass: 8490.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40204 #27: Protein | Mass: 9669.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P54999 #28: Protein | Mass: 12876.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06217 #30: Protein | Mass: 11240.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P43321 |
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-Non-polymers , 4 types, 14 molecules ![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
#32: Chemical | ChemComp-IHP / | ||
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#33: Chemical | ChemComp-GTP / | ||
#34: Chemical | ChemComp-MG / #35: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: catalytically activated spliceosome B*-a2 complex / Type: COMPLEX / Entity ID: #1-#31 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.9 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Electron dose: 49.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 555036 / Symmetry type: POINT |