4IFD

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

  • Classification: HYDROLASE / RNA
  • Deposited: 2012-12-14 Released: 2013-02-06
  • Deposition author(s): Makino, D.L.Conti, E.
  • 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, Escherichia coli
  • Mutation(s): 7

Structural Biology Knowledgebase: 4IFD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IFD

Classification: HYDROLASE / RNA

Total Structure Weight: 438165.92


Macromolecule Entities
Molecule Chains Length Organism Details
Exosome complex component RRP45 A 304 Saccharomyces cerevisiae Gene Name(s): RRP45 YDR280W D9954.1
Exosome complex component SKI6 B 248 Saccharomyces cerevisiae Gene Name(s): SKI6 ECM20 RRP41 YGR195W G7587
Exosome complex component RRP43 C 393 Saccharomyces cerevisiae Mutation: A102S, V363M
Gene Name(s): RRP43 YCR035C YCR35C YCR522
Exosome complex component RRP46 D 245 Saccharomyces cerevisiae Gene Name(s): RRP46 YGR095C
Exosome complex component RRP42 E 267 Saccharomyces cerevisiae Mutation: V138I
Gene Name(s): RRP42 YDL111C
Exosome complex component MTR3 F 250 Saccharomyces cerevisiae Mutation: T75S, M161T
Gene Name(s): MTR3 YGR158C G6676
Exosome complex component RRP40 G 242 Saccharomyces cerevisiae Gene Name(s): RRP40 YOL142W
Exosome complex component RRP4 H 361 Saccharomyces cerevisiae Gene Name(s): RRP4 YHR069C
Exosome complex component CSL4 I 301 Saccharomyces cerevisiae Gene Name(s): CSL4 SKI4 YNL232W N1154
Exosome complex exonuclease DIS3 J 1003 Saccharomyces cerevisiae EC#: 3.1.13 IUBMB 3.1.26 IUBMB
Mutation: D171N, D551N
Gene Name(s): DIS3 Gene View RRP44 YOL021C O2197
Exosome complex exonuclease RRP6 K 179 Saccharomyces cerevisiae EC#: 3.1.13 IUBMB
Fragment: UNP RESIDUES 518-693
Gene Name(s): RRP6 UNC733 YOR001W
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (45-MER) R 45 synthetic

Small Molecules
Ligands 5 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)
GOL
Query on GOL

C, G, H GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BR
Query on BR

A, E, F, H, I, J BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

J ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.183
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 154.09 α = 90.00
b = 107.44 β = 110.63
c = 150.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-14
  • Released Date: 2013-02-06
  • Deposition author(s): Makino, D.L., Conti, E.

Revision History

  • 2013-11-13
    Type: Citation | Details: Citation update
  • 2013-03-13
    Type: Citation | Details: Citation update