5VZJ

STRUCTURE OF A TWELVE COMPONENT MPP6-NUCLEAR RNA EXOSOME COMPLEX BOUND TO RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.217

Literature

Macromolecules
Sequence Display for 5VZJ

Classification: HYDROLASE / RNA

Total Structure Weight: 479983.22


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 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 559 Saccharomyces cerevisiae EC#: 3.1.13 IUBMB
Fragment: UNP residues 129-684
Mutation: D238N
Gene Name(s): RRP6 UNC733 YOR001W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exosome complex exonuclease DIS3 K 1003 Saccharomyces cerevisiae EC#: 3.1.13 IUBMB 3.1.26 IUBMB
Mutation: D171N, D551N
Gene Name(s): DIS3 Gene View RRP44 YOL021C O2197
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
M-phase phosphoprotein 6 homolog L 42 Saccharomyces cerevisiae Fragment: UNP residues 81-120
Gene Name(s): MPP6 Gene View YNR024W N3230
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (11-MER) M 11 Homo sapiens
RNA (19-MER) N 19 Homo sapiens

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B, G, K SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, K GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

K ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.217
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 141.09 α = 90.00
b = 213.59 β = 90.00
c = 225.91 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-05-28
  • Released Date: 2017-08-02
  • Deposition author(s): Lima, C.D., Wasmuth, E.V.

Revision History

  • Version 1_0: 2017-08-02

    Type: Initial release

  • Version 1_1: 2017-08-09

    Type: Database references