4OO1

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

  • Classification: HYDROLASE / RNA
  • Deposited: 2014-01-29 Released: 2014-07-02
  • Deposition author(s): Lima, C.D.Wasmuth, E.V.
  • Organism: Saccharomyces cerevisiae
  • Expression System: Escherichia coli, Escherichia coli, Escherichia coli, Escherichia coli, Escherichia coli, Escherichia coli, Escherichia coli, Escherichia coli, Escherichia coli, Escherichia coli
  • Mutation(s): 1

Structural Biology Knowledgebase: 4OO1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.227

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4OO1

Classification: HYDROLASE / RNA

Total Structure Weight: 359659.31


Macromolecule Entities
Molecule Chains Length Organism Details
Exosome complex component RRP45 A 305 Saccharomyces cerevisiae Gene Name(s): RRP45 YDR280W D9954.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex component SKI6 B 250 Saccharomyces cerevisiae Gene Name(s): SKI6 ECM20 RRP41 YGR195W G7587
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex component RRP43 C 394 Saccharomyces cerevisiae Gene Name(s): RRP43 YCR035C YCR35C YCR522
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex component RRP46 D 225 Saccharomyces cerevisiae Gene Name(s): RRP46 YGR095C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex component RRP42 E 269 Saccharomyces cerevisiae Gene Name(s): RRP42 YDL111C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex component MTR3 F 250 Saccharomyces cerevisiae EC#: 3.1.13 IUBMB
Gene Name(s): MTR3 YGR158C G6676
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex component RRP40 G 244 Saccharomyces cerevisiae Gene Name(s): RRP40 YOL142W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex component RRP4 H 363 Saccharomyces cerevisiae Gene Name(s): RRP4 YHR069C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex component CSL4 I 296 Saccharomyces cerevisiae Gene Name(s): CSL4 SKI4 YNL232W N1154
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex exonuclease RRP6 J 560 Saccharomyces cerevisiae EC#: 3.1.13 IUBMB
Mutation: D238N
Gene Name(s): RRP6 UNC733 YOR001W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
POLY A RNA S 24 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MES
Query on MES

G 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

E (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

I, S PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

E, S MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.227
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 193.29 α = 90.00
b = 200.08 β = 90.00
c = 97.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-01-29
  • Released Date: 2014-07-02
  • Deposition author(s): Lima, C.D., Wasmuth, E.V.

Revision History

  • 2014-08-27
    Type: Citation | Details: Citation update