+Open data
-Basic information
Entry | Database: PDB / ID: 5g06 | ||||||
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Title | Cryo-EM structure of yeast cytoplasmic exosome | ||||||
Components |
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Keywords | HYDROLASE / RNA DECAY / EXOSOME / RNA QUALITY CONTROL | ||||||
Function / homology | Function and homology information Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / U4 snRNA 3'-end processing / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, non-stop decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / translational elongation / translation elongation factor activity / RNA processing / RNA endonuclease activity / protein catabolic process / mRNA processing / manganese ion binding / protein-macromolecule adaptor activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / endonuclease activity / tRNA binding / translation / GTPase activity / protein-containing complex binding / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Liu, J.J. / Niu, C.Y. / Wu, Y. / Tan, D. / Wang, Y. / Ye, M.D. / Liu, Y. / Zhao, W.W. / Zhou, K. / Liu, Q.S. ...Liu, J.J. / Niu, C.Y. / Wu, Y. / Tan, D. / Wang, Y. / Ye, M.D. / Liu, Y. / Zhao, W.W. / Zhou, K. / Liu, Q.S. / Dai, J.B. / Yang, X.R. / Dong, M.Q. / Huang, N. / Wang, H.W. | ||||||
Citation | Journal: Cell Res / Year: 2016 Title: CryoEM structure of yeast cytoplasmic exosome complex. Authors: Jun-Jie Liu / Chu-Ya Niu / Yao Wu / Dan Tan / Yang Wang / Ming-Da Ye / Yang Liu / Wenwei Zhao / Ke Zhou / Quan-Sheng Liu / Junbiao Dai / Xuerui Yang / Meng-Qiu Dong / Niu Huang / Hong-Wei Wang / Abstract: The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. ...The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "GC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "GC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5g06.cif.gz | 608.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g06.ent.gz | 473.6 KB | Display | PDB format |
PDBx/mmJSON format | 5g06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g06_validation.pdf.gz | 817.6 KB | Display | wwPDB validaton report |
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Full document | 5g06_full_validation.pdf.gz | 944.3 KB | Display | |
Data in XML | 5g06_validation.xml.gz | 99.7 KB | Display | |
Data in CIF | 5g06_validation.cif.gz | 148.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/5g06 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/5g06 | HTTPS FTP |
-Related structure data
Related structure data | 3366MC 3367C 3368C 3369C 3370C 3371C 3372C 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
-EXOSOME COMPLEX COMPONENT ... , 9 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 34001.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q05636 |
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#2: Protein | Mass: 27599.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P46948 |
#3: Protein | Mass: 44093.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P25359 |
#4: Protein | Mass: 24430.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P53256 |
#5: Protein | Mass: 29099.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q12277 |
#6: Protein | Mass: 27589.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P48240 |
#7: Protein | Mass: 26583.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q08285 |
#8: Protein | Mass: 39470.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38792 |
#9: Protein | Mass: 31619.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P53859 |
-Protein , 2 types, 2 molecules JP
#10: Protein | Mass: 113855.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q08162, exoribonuclease II |
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#11: Protein | Mass: 84888.695 Da / Num. of mol.: 1 / Fragment: N TERMINAL FRAGMENT / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q08491 |
-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: RNA-FREE EXO10-SKI7 / Type: COMPLEX |
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Buffer solution | Name: 150MM NACL, 50MM TRIS-HCL, 1MM EGTA,1MMDTT / pH: 8 / Details: 150MM NACL, 50MM TRIS-HCL, 1MM EGTA,1MMDTT |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Oct 20, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 21 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Details: MICROGRAPHS | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Num. of particles: 25000 / Nominal pixel size: 1.32 Å / Actual pixel size: 1.30564 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3366. (DEPOSITION ID: 14342). Symmetry type: POINT | ||||||||||||||||
Refinement | Highest resolution: 4.2 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.2 Å
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