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- PDB-7dco: Cryo-EM structure of the activated spliceosome (Bact complex) at ... -
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Basic information
Entry | Database: PDB / ID: 7dco | ||||||
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Title | Cryo-EM structure of the activated spliceosome (Bact complex) at an atomic resolution of 2.5 angstrom | ||||||
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![]() | SPLICING / RNA splicing / spliceosome / Bact complex / Prp2 / Spp2 / ATPase/helicase / activation | ||||||
Function / homology | ![]() maintenance of RNA location / RES complex / snoRNA splicing / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / Prp19 complex / ATP-dependent activity, acting on RNA / small nuclear ribonucleoprotein complex ...maintenance of RNA location / RES complex / snoRNA splicing / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / Prp19 complex / ATP-dependent activity, acting on RNA / 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 / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / regulation of RNA splicing / mRNA 5'-splice site recognition / ATPase activator activity / U5 snRNA binding / U5 snRNP / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nucleic acid binding / RNA helicase activity / RNA helicase / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
![]() | Bai, R. / Wan, R. / Yan, C. / Qi, J. / Zhang, P. / Lei, J. / Shi, Y. | ||||||
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![]() | ![]() Title: Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Qi Jia / Jianlin Lei / Yigong Shi / ![]() Abstract: Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the ...Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the function of the ATPase/helicases remains poorly understood. Here, we report atomic structures of Prp2 in isolation, Prp2 complexed with its coactivator Spp2, and Prp2-loaded activated spliceosome and the results of structure-guided biochemical analysis. Prp2 weakly associates with the spliceosome and cannot function without Spp2, which stably associates with Prp2 and anchors on the spliceosome, thus tethering Prp2 to the activated spliceosome and allowing Prp2 to function. Pre-mRNA is loaded into a featured channel between the N and C halves of Prp2, where Leu from the N half and Arg from the C half prevent backward sliding of pre-mRNA toward its 5'-end. Adenosine 5'-triphosphate binding and hydrolysis trigger interdomain movement in Prp2, which drives unidirectional stepwise translocation of pre-mRNA toward its 3'-end. These conserved mechanisms explain the coupling of spliceosome remodeling to pre-mRNA splicing. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30637MC ![]() 7dcpC ![]() 7dcqC ![]() 7dcrC ![]() 7dd3C 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
+Protein , 27 types, 31 molecules ACDahbmcnfjopuv123456KNTYXWVzJI
-RNA chain , 4 types, 4 molecules BFGH
#2: RNA chain | Mass: 68643.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#12: RNA chain | Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: RNA chain | Mass: 44772.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: RNA chain | Mass: 376324.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Small nuclear ribonucleoprotein ... , 4 types, 6 molecules deigkl
#5: Protein | Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#9: Protein | Mass: 10385.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: 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 #17: Protein | | Mass: 8882.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Pre-mRNA-splicing factor ... , 10 types, 10 molecules wLQRSZUMyx
#19: Protein | Mass: 33111.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32524 |
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#27: 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 |
#33: Protein | Mass: 40988.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#34: Protein | Mass: 29742.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#35: 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 |
#38: Protein | Mass: 14039.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 15793.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#42: Protein | Mass: 29797.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#44: Protein | Mass: 20685.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02521 |
#47: Protein | Mass: 99947.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P20095, RNA helicase |
-Pre-mRNA-processing ... , 2 types, 5 molecules stqrP
#28: Protein | Mass: 56629.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A6A5PQI0, RING-type E3 ubiquitin transferase #32: Protein | | Mass: 42548.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 1738 molecules ![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#48: Chemical | ChemComp-IHP / | ||||||
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#49: Chemical | ChemComp-GTP / | ||||||
#50: Chemical | ChemComp-MG / #51: Chemical | ChemComp-CA / | #52: Chemical | ChemComp-ZN / #53: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-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: the activated spliceosome Bact complex / Type: COMPLEX / Entity ID: #1-#50 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil |
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 |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 705371 / Symmetry type: POINT |