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- PDB-5gm6: Cryo-EM structure of the activated spliceosome (Bact complex) at ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gm6 | ||||||
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Title | Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution | ||||||
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![]() | RNA BINDING PROTEIN/RNA / ![]() ![]() ![]() | ||||||
Function / homology | ![]() maintenance of RNA location / RES complex / response to xenobiotic stimulus / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / snoRNA splicing / cellular bud site selection / cis assembly of pre-catalytic spliceosome / post-mRNA release spliceosomal complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, C. / Wan, R. / Bai, R. / Huang, G. / Shi, Y. | ||||||
![]() | ![]() Title: Structure of a yeast activated spliceosome at 3.5 Å resolution. Authors: Chuangye Yan / Ruixue Wan / Rui Bai / Gaoxingyu Huang / Yigong Shi / ![]() Abstract: Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome ...Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3.52 angstroms. The final refined model contains U2 and U5 small nuclear ribonucleoprotein particles (snRNPs), U6 small nuclear RNA (snRNA), nineteen complex (NTC), NTC-related (NTR) protein, and a 71-nucleotide pre-mRNA molecule, which amount to 13,505 amino acids from 38 proteins and a combined molecular mass of about 1.6 megadaltons. The 5' exon is anchored by loop I of U5 snRNA, whereas the 5' splice site (5'SS) and the branch-point sequence (BPS) of the intron are specifically recognized by U6 and U2 snRNA, respectively. Except for coordination of the catalytic metal ions, the RNA elements at the catalytic cavity of Prp8 are mostly primed for catalysis. The catalytic latency is maintained by the SF3b complex, which encircles the BPS, and the splicing factors Cwc24 and Prp11, which shield the 5' exon-5'SS junction. This structure, together with those determined earlier, outlines a molecular framework for the pre-mRNA splicing reaction. | ||||||
Validation Report | ![]() ![]() ![]() | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmcif format | ![]() ![]() ![]() |
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-Related structure data
Related structure data | ![]() 9524CM C: citing same article ( M: map data used to model this data |
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Similar-shape strucutres |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Pre-mRNA-splicing factor ... , 20 types, 20 molecules ACFIJOQRSTWYZacdXvft
+Protein , 8 types, 8 molecules BHKPUbek
+Saccharomyces cerevisiae strain ... , 2 types, 2 molecules DE
+RNA chain , 3 types, 3 molecules LNM
+U2 snRNP component ... , 2 types, 2 molecules VG
+Pre-mRNA-processing factor ... , 2 types, 5 molecules opqrn
+Small nuclear ribonucleoprotein ... , 6 types, 6 molecules ihjlmg
+Non-polymers , 4 types, 20 molecules 






+Details
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Bact spliceosomal complex / Type: COMPLEX / Entity ID: #1-#43 / Source: NATURAL |
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Molecular weight | Value: 2.0 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 8 Details: CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA) |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
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: 4.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Scanner model: OTHER |
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Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction![]() | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77312 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL |
Refinement | Highest resolution: 3.5 Å |