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Yorodumi- PDB-7dd3: Cryo-EM structure of the pre-mRNA-loaded DEAH-box ATPase/helicase... -
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-Basic information
Entry | Database: PDB / ID: 7dd3 | ||||||
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Title | Cryo-EM structure of the pre-mRNA-loaded DEAH-box ATPase/helicase Prp2 in complex with Spp2 | ||||||
Components |
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Keywords | SPLICING / RNA splicing / spliceosome / Bact complex / Prp2 / Spp2 / DEAH-box ATPase/helicase | ||||||
Function / homology | Function and homology information snoRNA splicing / generation of catalytic spliceosome for first transesterification step / ATP-dependent activity, acting on RNA / U2-type catalytic step 1 spliceosome / ATPase activator activity / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity ...snoRNA splicing / generation of catalytic spliceosome for first transesterification step / ATP-dependent activity, acting on RNA / U2-type catalytic step 1 spliceosome / ATPase activator activity / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.2 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
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 7dd3.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dd3.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dd3_validation.pdf.gz | 735.2 KB | Display | wwPDB validaton report |
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Full document | 7dd3_full_validation.pdf.gz | 736.4 KB | Display | |
Data in XML | 7dd3_validation.xml.gz | 24 KB | Display | |
Data in CIF | 7dd3_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/7dd3 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/7dd3 | HTTPS FTP |
-Related structure data
Related structure data | 30643MC 7dcoC 7dcpC 7dcqC 7dcrC 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
#1: Protein | Mass: 99947.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q5S8, UniProt: P20095*PLUS |
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#2: Protein | Mass: 20685.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q6Y7, UniProt: Q02521*PLUS |
#3: RNA chain | Mass: 2710.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-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 complex of pre-mRNA-loaded DEAH-box ATPase/helicase Prp2 and its coactivator Spp2 Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES |
EM staining | Type: NEGATIVE / Material: Uranyl Acetate |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 45 e/Å2 / 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 556393 / Symmetry type: POINT |