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Yorodumi- PDB-5gmk: Cryo-EM structure of the Catalytic Step I spliceosome (C complex)... -
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-Basic information
Entry | Database: PDB / ID: 5gmk | |||||||||
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Title | Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA splicing / Spliceosome / Catalytic Step I / Intron lariat / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / cellular bud site selection / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / pre-mRNA binding ...post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / cellular bud site selection / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / Prp19 complex / U4 snRNP / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type catalytic step 2 spliceosome / U2 snRNP / poly(U) RNA binding / U1 snRNP / spliceosomal complex assembly / U2-type prespliceosome / spliceosomal snRNP assembly / precatalytic spliceosome / Dual incision in TC-NER / DNA replication origin binding / generation of catalytic spliceosome for second transesterification step / Gap-filling DNA repair synthesis and ligation in TC-NER / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / DNA replication initiation / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / positive regulation of cell cycle / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / translation elongation factor activity / catalytic step 2 spliceosome / nuclear periphery / positive regulation of RNA splicing / RNA splicing / mRNA splicing, via spliceosome / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / metallopeptidase activity / cell cycle / DNA repair / GTPase activity / mRNA binding / chromatin binding / chromatin / GTP binding / mitochondrion / DNA binding / RNA binding / metal ion binding / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wan, R. / Yan, C. / Bai, R. / Huang, G. / Shi, Y. | |||||||||
Citation | Journal: Science / Year: 2016 Title: Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution. Authors: Ruixue Wan / Chuangye Yan / Rui Bai / Gaoxingyu Huang / Yigong Shi / Abstract: Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. ...Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. Here we report an atomic structure of a catalytic step I spliceosome (known as the C complex) from Saccharomyces cerevisiae, as determined by cryo-electron microscopy at an average resolution of 3.4 angstroms. In the structure, the 2'-OH of the invariant adenine nucleotide in the branch point sequence (BPS) is covalently joined to the phosphate at the 5' end of the 5' splice site (5'SS), forming an intron lariat. The freed 5' exon remains anchored to loop I of U5 small nuclear RNA (snRNA), and the 5'SS and BPS of the intron form duplexes with conserved U6 and U2 snRNA sequences, respectively. Specific placement of these RNA elements at the catalytic cavity of Prp8 is stabilized by 15 protein components, including Snu114 and the splicing factors Cwc21, Cwc22, Cwc25, and Yju2. These features, representing the conformation of the spliceosome after the first-step reaction, predict structural changes that are needed for the execution of the second-step transesterification reaction. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 5gmk.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5gmk.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5gmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/5gmk ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gmk | HTTPS FTP |
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-Related structure data
Related structure data | 9525MC 9526C 9527C 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
-Pre-mRNA-splicing factor ... , 16 types, 16 molecules ACJOQRSTZcdGHIvt
#1: Protein | Mass: 279867.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: 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) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P36048 |
#9: Protein | Mass: 15793.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q03375 |
#10: Protein | Mass: 50771.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q12417 |
#12: Protein | Mass: 40988.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P38241 |
#13: Protein | Mass: 38486.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q12046 |
#14: Protein | Mass: 19975.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q03772 |
#15: Protein | Mass: 18484.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P25337 |
#16: Protein | Mass: 67386.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P53333 |
#17: Protein | Mass: 61057.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q03654 |
#18: Protein | Mass: 68044.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q12309 |
#20: Protein | Mass: 20412.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P53854 |
#21: Protein | Mass: 28073.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P21374 |
#22: Protein | Mass: 24850.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P53277 |
#23: Protein | Mass: 78125.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae S288c (yeast), (natural) Saccharomyces cerevisiae S288C (yeast) Strain: S288c / References: UniProt: Q04048 |
#26: Protein | Mass: 20741.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q06091 |
-RNA chain , 6 types, 6 molecules DELMBN
#3: RNA chain | Mass: 68643.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) |
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#4: RNA chain | Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) |
#5: RNA chain | Mass: 376267.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) |
#6: RNA chain | Mass: 9161.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) |
#7: RNA chain | Mass: 4112.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) |
#8: RNA chain | Mass: 4694.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) |
-Protein , 3 types, 4 molecules PFks
#11: Protein | Mass: 42548.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P28004 |
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#19: Protein | Mass: 32371.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P28320 |
#27: Protein | Mass: 22426.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P40018 |
-Pre-mRNA-processing factor ... , 2 types, 5 molecules nopqr
#24: Protein | Mass: 52128.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P40968 |
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#25: Protein | Mass: 56629.777 Da / Num. of mol.: 4 / Mutation: Q315S, I317E / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c References: UniProt: P32523, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules iuhwjxlymzge
#28: Protein | Mass: 10385.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q12330 #29: Protein | Mass: 9669.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P54999 #30: Protein | Mass: 8490.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P40204 #31: Protein | Mass: 11240.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P43321 #32: Protein | Mass: 16296.798 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q02260 #33: Protein | Mass: 12876.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q06217 |
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-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules ab
#34: Protein | Mass: 12850.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P40567 |
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#35: Protein | Mass: 27232.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q08963 |
-Non-polymers , 3 types, 14 molecules
#36: Chemical | ChemComp-GTP / | ||
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#37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-ZN / |
-Details
Sequence details | EACH SEQUENCE OF THE c(LOWER-CASE)/d(lower-case)/v(lower-case) CHAINS CORRESPONDS TO EACH UNP ...EACH SEQUENCE OF THE c(LOWER-CASE)/d(lower-case)/v(lower-case) CHAINS CORRESPOND |
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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: Spliceosomal C Complex / Type: COMPLEX / Entity ID: #1-#35 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Buffer solution | pH: 8 Details: The 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: NO / Vitrification applied: YES |
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 FIELDBright-field microscopy |
Image recording | Electron dose: 4.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Scanner model: OTHER |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161066 / Symmetry type: POINT |
Refinement | Highest resolution: 3.4 Å |