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Yorodumi- PDB-3jb9: Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jb9 | |||||||||
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Title | Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Spliceosome / U2/U5/U6 / Lariat / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information : / : / : / : / protein modification by small protein conjugation or removal / regulation of siRNA-mediated facultative heterochromatin formation / Transport of Mature mRNA derived from an Intron-Containing Transcript / second spliceosomal transesterification activity / : / Dual incision in TC-NER ...: / : / : / : / protein modification by small protein conjugation or removal / regulation of siRNA-mediated facultative heterochromatin formation / Transport of Mature mRNA derived from an Intron-Containing Transcript / second spliceosomal transesterification activity / : / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / spliceosomal conformational changes to generate catalytic conformation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U12-type spliceosomal complex / Prp19 complex / pICln-Sm protein complex / Cul4-RING E3 ubiquitin ligase complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / cell cycle / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / protein peptidyl-prolyl isomerization / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / nuclear envelope / metallopeptidase activity / ubiquitin protein ligase activity / protein folding / cysteine-type deubiquitinase activity / ribonucleoprotein complex / DNA repair / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Yan, C. / Hang, J. / Wan, R. / Huang, M. / Wong, C. / Shi, Y. | |||||||||
Citation | Journal: Science / Year: 2015 Title: Structure of a yeast spliceosome at 3.6-angstrom resolution. Authors: Chuangye Yan / Jing Hang / Ruixue Wan / Min Huang / Catherine C L Wong / Yigong Shi / Abstract: Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins ...Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of 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 | 3jb9.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jb9.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 3jb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jb9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3jb9_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3jb9_validation.xml.gz | 222.9 KB | Display | |
Data in CIF | 3jb9_validation.cif.gz | 379.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jb9 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jb9 | HTTPS FTP |
-Related structure data
Related structure data | 6413MC 6414MC 6415MC 6416MC 6417MC 6418MC 6419MC 6420MC 6421MC 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 ... , 14 types, 14 molecules ABKLWYacehiRrX
#1: Protein | Mass: 274917.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O14187 |
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#2: Protein | Mass: 111445.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O94316 |
#11: Protein | Mass: 48909.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O13615 |
#12: Protein | Mass: 37477.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O94620 |
#19: Protein | Mass: 75128.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P39964 |
#20: Protein | Mass: 41838.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P87126 |
#21: Protein | Mass: 37133.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O59800 |
#22: Protein | Mass: 74547.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q09909 |
#24: Protein | Mass: 17122.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O74772 |
#26: Protein | Mass: 30478.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P78794 |
#27: Protein | Mass: 21348.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9USV3 |
#28: Protein | Mass: 67082.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P87312 |
#29: Protein | Mass: 72172.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9P7R9 |
#30: Protein | Mass: 148532.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O94508 |
-RNA chain , 5 types, 5 molecules CNOQP
#3: RNA chain | Mass: 38191.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) |
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#14: RNA chain | Mass: 31863.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) |
#15: RNA chain | Mass: 2528.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) |
#16: RNA chain | Mass: 4047.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: chain O and Q come from one RNA molecule. atom O2' A (Q 501) is covalently binding to atom P G (Q 100). Source: (natural) Schizosaccharomyces pombe (fission yeast) |
#17: RNA chain | Mass: 59207.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules DZFfGlHmInJo
#4: Protein | Mass: 11050.884 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9UUC6 #6: Protein | Mass: 13115.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O42661 #7: Protein | Mass: 13119.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O14036 #8: Protein | Mass: 9702.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9USZ3 #9: Protein | Mass: 8667.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O59734 #10: Protein | Mass: 8616.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O74966 |
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-Protein , 6 types, 7 molecules EbMdjkx
#5: Protein | Mass: 15493.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q10163 #13: Protein | | Mass: 62798.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q09882 #23: Protein | | Mass: 16884.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: P87051, peptidylprolyl isomerase #31: Protein | | Mass: 27260.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q9USX8 #32: Protein | | Mass: 12685.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: Q7LL14 #33: Protein | | Mass: 35081.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
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-Pre-mRNA-processing factor ... , 2 types, 5 molecules STUVg
#18: Protein | Mass: 54243.988 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 References: UniProt: O14011, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #25: Protein | | Mass: 63211.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 / References: UniProt: O43071 |
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-Non-polymers , 4 types, 13 molecules
#34: Chemical | ChemComp-GDP / | ||||
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#35: Chemical | ChemComp-MG / #36: Chemical | ChemComp-ZN / #37: Chemical | ChemComp-ADP / | |
-Details
Sequence details | THERE ARE MANY UNK RESIDUES IN CHAIN K, W, Y, a(LOWER CASE), R, r(LOWER CASE). THE COMPLETE ...THERE ARE MANY UNK RESIDUES IN CHAIN K, W, Y, a(LOWER CASE), R, r(LOWER CASE). THE COMPLETE SEQUENCE OF THESE 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: spliceosome / Type: COMPLEX |
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Buffer solution | Name: CEB buffer / pH: 8 / Details: CEB buffer |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: carbon coated grid |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 2.5 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Mar 29, 2015 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1.5 nm / Nominal defocus min: 3 nm / Cs: 1.4 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: GATAN K2 (4k x 4k) |
-Processing
EM software | Name: RELION / Category: 3D reconstruction | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112795 / Details: (Single particle--Applied symmetry: C1) / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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