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Yorodumi- PDB-7dco: Cryo-EM structure of the activated spliceosome (Bact complex) at ... -
+Open data
-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 | ||||||
Components |
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Keywords | SPLICING / RNA splicing / spliceosome / Bact complex / Prp2 / Spp2 / ATPase/helicase / activation | ||||||
Function / homology | Function and homology information maintenance of RNA location / RES complex / protein serine/threonine phosphatase inhibitor activity / snoRNA splicing / negative regulation of protein dephosphorylation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / miRNA processing / U4/U6 snRNP / Prp19 complex ...maintenance of RNA location / RES complex / protein serine/threonine phosphatase inhibitor activity / snoRNA splicing / negative regulation of protein dephosphorylation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / miRNA processing / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation / pre-mRNA binding / U2-type catalytic step 1 spliceosome / ATP-dependent activity, acting on RNA / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / 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 alternative mRNA splicing, via spliceosome / mRNA 5'-splice site recognition / regulation of RNA splicing / ATPase activator activity / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / mRNA export from nucleus / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / helicase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / nuclear speck / 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
Authors | Bai, R. / Wan, R. / Yan, C. / Qi, J. / Zhang, P. / Lei, J. / Shi, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Science / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7dco.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7dco.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7dco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dco_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7dco_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7dco_validation.xml.gz | 346.2 KB | Display | |
Data in CIF | 7dco_validation.cif.gz | 588.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/7dco ftp://data.pdbj.org/pub/pdb/validation_reports/dc/7dco | HTTPS FTP |
-Related structure data
Related structure data | 30637MC 7dcpC 7dcqC 7dcrC 7dd3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039023403 |
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#12: RNA chain | Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039022925 |
#13: RNA chain | Mass: 44772.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#14: RNA chain | Mass: 376324.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3H8 | ||||
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#9: Protein | Mass: 10385.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q895 #11: Protein | Mass: 8490.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3H8 |
-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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0Z2 |
#34: Protein | Mass: 29742.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q155 |
#35: Protein | Mass: 19975.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L1AYM3 |
#40: Protein | Mass: 15793.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZG6 |
#42: Protein | Mass: 29797.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PVM6 |
#44: Protein | Mass: 20685.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (brewer's yeast) 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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTY9 |
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-Non-polymers , 6 types, 1738 molecules
#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 |
-Sample preparation
Component | Name: the activated spliceosome Bact complex / Type: COMPLEX / Entity ID: #1-#50 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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 |