5JEA Hydrolase Rna date Apr 18, 2016
title Structure Of A Cytoplasmic 11-Subunit Rna Exosome Complex In Ski7, Bound To Rna
authors E.Kowalinski, J.Ebert, E.Stegmann, E.Conti
compound source
Molecule: Exosome Complex Component Rrp45
Chain: A
Synonym: Ribosomal Rna-Processing Protein 45
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rrp45, Ydr280w, D9954.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Ski6
Chain: B
Synonym: Extracellular Mutant Protein 20,Ribosomal Rna-Proc Protein 41,Superkiller Protein 6;
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Ski6, Ecm20, Rrp41, Ygr195w, G7587
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp43
Chain: C
Synonym: Ribosomal Rna-Processing Protein 43
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rrp43, Ycr035c, Ycr35c, Ycr522
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp46
Chain: D
Synonym: Ribosomal Rna-Processing Protein 46
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rrp46, Ygr095c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp42
Chain: E
Synonym: Ribosomal Rna-Processing Protein 42
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rrp42, Ydl111c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Mtr3
Chain: F
Synonym: Mrna Transport Regulator 3
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Mtr3, Ygr158c, G6676
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp40
Chain: G
Synonym: Ribosomal Rna-Processing Protein 40
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rrp40, Yol142w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp4
Chain: H
Synonym: Ribosomal Rna-Processing Protein 4
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rrp4, Yhr069c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Csl4
Chain: I
Synonym: Cep1 Synthetic Lethal Protein 4
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Csl4, Ski4, Ynl232w, N1154
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Exonuclease Dis3
Chain: J
Synonym: Chromosome Disjunction Protein 3,Ribosomal Rna-Pro Protein 44;
Ec: 3.1.13.-,3.1.26.-
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Dis3, Rrp44, Yol021c, O2197
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Superkiller Protein 7,Endolysin
Chain: K
Synonym: Lysis Protein,Lysozyme,Muramidase
Ec: 3.2.1.17
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae, Enterobacter T4;
Organism_common: Baker'S Yeast
Organism_taxid: 559292, 10665
Strain: Atcc 204508 S288c
Gene: Ski7, Yor076c, Yor29-27
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (29-Mer)
Chain: R
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.215 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.080 182.530 250.550 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand MPD, NA, ZN enzyme Hydrolase E.C.3.1.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • B

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • C

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • D

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • E

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • F

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • G

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • H


    I

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • J
  • endoribonuclease activity

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
    • K


    Primary referenceStructure of a Cytoplasmic 11-Subunit RNA Exosome Complex., Kowalinski E, Kogel A, Ebert J, Reichelt P, Stegmann E, Habermann B, Conti E, Mol Cell. 2016 Jul 7;63(1):125-34. doi: 10.1016/j.molcel.2016.05.028. Epub 2016, Jun 23. PMID:27345150
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1127 Kb) [Save to disk]
  • Biological Unit Coordinates (5jea.pdb1.gz) 1116 Kb
  • LPC: Ligand-Protein Contacts for 5JEA
  • CSU: Contacts of Structural Units for 5JEA
  • Structure Factors (3657 Kb)
  • Retrieve 5JEA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JEA from S2C, [Save to disk]
  • Re-refined 5jea structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JEA in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5JEA
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jea_G] [5jea_B] [5jea_D] [5jea] [5jea_I] [5jea_E] [5jea_J] [5jea_F] [5jea_A] [5jea_C] [5jea_R] [5jea_K] [5jea_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JEA: [PINc] [RNB] [S1 ] by SMART
    • Other resources with information on 5JEA
  • Community annotation for 5JEA at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science