[English] 日本語
Yorodumi
- PDB-5g06: Cryo-EM structure of yeast cytoplasmic exosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g06
TitleCryo-EM structure of yeast cytoplasmic exosome
Components
  • (EXOSOME COMPLEX COMPONENT ...) x 9
  • EXOSOME COMPLEX EXONUCLEASE DIS3
  • SUPERKILLER PROTEIN 7
KeywordsHYDROLASE / RNA DECAY / EXOSOME / RNA QUALITY CONTROL
Function / homology
Function and homology information


Eukaryotic Translation Elongation / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / cytoplasmic exosome (RNase complex) ...Eukaryotic Translation Elongation / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / 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) / : / HSF1 activation / rRNA catabolic process / nuclear mRNA surveillance / nonfunctional rRNA decay / Protein methylation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / translational elongation / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / RNA processing / translation elongation factor activity / RNA endonuclease activity / Neutrophil degranulation / protein catabolic process / mRNA processing / protein-macromolecule adaptor activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / manganese ion binding / 3'-5'-RNA exonuclease activity / endonuclease activity / tRNA binding / translation / GTPase activity / protein-containing complex binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / RRP4, S1 domain / Exosome complex component RRP45 / Rrp40, S1 domain / : ...: / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / RRP4, S1 domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / PIN domain / : / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Large family of predicted nucleotide-binding domains / PIN domain / K Homology domain, type 1 / K Homology domain, type 1 superfamily / PIN-like domain superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / Superkiller protein 7 / Exosome complex component RRP42
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLiu, 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.
CitationJournal: 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
DepositionMar 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references / Other
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
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
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3366
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXOSOME COMPLEX COMPONENT RRP45
B: EXOSOME COMPLEX COMPONENT SKI6
C: EXOSOME COMPLEX COMPONENT RRP43
D: EXOSOME COMPLEX COMPONENT RRP46
E: EXOSOME COMPLEX COMPONENT RRP42
F: EXOSOME COMPLEX COMPONENT MTR3
G: EXOSOME COMPLEX COMPONENT RRP40
H: EXOSOME COMPLEX COMPONENT RRP4
I: EXOSOME COMPLEX COMPONENT CSL4
J: EXOSOME COMPLEX EXONUCLEASE DIS3
P: SUPERKILLER PROTEIN 7


Theoretical massNumber of molelcules
Total (without water)483,23111
Polymers483,23111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
EXOSOME COMPLEX COMPONENT ... , 9 types, 9 molecules ABCDEFGHI

#1: Protein EXOSOME COMPLEX COMPONENT RRP45 / / RIBOSOMAL RNA-PROCESSING PROTEIN 45


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
#2: Protein EXOSOME COMPLEX COMPONENT SKI6 / / EXTRACELLULAR MUTANT PROTEIN 20 / RIBOSOMAL RNA-PROCESSING PROTEIN 41 / SUPERKILLER PROTEIN 6


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 EXOSOME COMPLEX COMPONENT RRP43 / / RIBOSOMAL RNA-PROCESSING PROTEIN 43


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 EXOSOME COMPLEX COMPONENT RRP46 / / RIBOSOMAL RNA-PROCESSING PROTEIN 46


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 EXOSOME COMPLEX COMPONENT RRP42 / / RIBOSOMAL RNA-PROCESSING PROTEIN 42


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 EXOSOME COMPLEX COMPONENT MTR3 / / MRNA TRANSPORT REGULATOR 3


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 EXOSOME COMPLEX COMPONENT RRP40 / / RIBOSOMAL RNA-PROCESSING PROTEIN 40


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 EXOSOME COMPLEX COMPONENT RRP4 / / RIBOSOMAL RNA-PROCESSING PROTEIN 4


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 EXOSOME COMPLEX COMPONENT CSL4 / / CEP1 SYNTHETIC LETHAL PROTEIN 4


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 EXOSOME COMPLEX EXONUCLEASE DIS3 / CHROMOSOME DISJUNCTION PROTEIN 3 / RIBOSOMAL RNA-PROCESSING PROTEIN 44


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
#11: Protein SUPERKILLER PROTEIN 7 / CYTOPLASMIC EXOSOME COMPONENT SKI7


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

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: RNA-FREE EXO10-SKI7 / Type: COMPLEX
Buffer solutionName: 150MM NACL, 50MM TRIS-HCL, 1MM EGTA,1MMDTT / pH: 8 / Details: 150MM NACL, 50MM TRIS-HCL, 1MM EGTA,1MMDTT
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 20, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Image recordingElectron dose: 21 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1EMAN23D reconstruction
2IMAGIC3D reconstruction
3RELION1.33D reconstruction
CTF correctionDetails: MICROGRAPHS
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 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
RefinementHighest resolution: 4.2 Å
Refinement stepCycle: LAST / Highest resolution: 4.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26794 0 0 0 26794

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more