4WFC

Structure of the Rrp6-Rrp47 interaction

• PDB DOI:  https://doi.org/10.2210/pdb4WFC/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-14 Released: 2014-10-29 
• Deposition Author(s): Schuch, B., Conti, E.
• Funding Organization(s): European Research Council, Marie Curie, German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.224 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.

Schuch, B., Feigenbutz, M., Makino, D.L., Falk, S., Basquin, C., Mitchell, P., Conti, E.

(2014) EMBO J 33: 2829-2846

• PubMed: 25319414 
• DOI: https://doi.org/10.15252/embj.201488757
• Primary Citation of Related Structures:  
  4WFC, 4WFD


• PubMed Abstract: 
  

The exosome is a conserved multi-subunit ribonuclease complex that functions in 3' end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10-subunit core complex of the exosome (Exo-10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo-10 in vitro is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N-terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N-terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C-terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6-Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.

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Organizational Affiliation: 

Structural Cell Biology Department, Max Planck Institute of Biochemistry, Martinsried, Germany [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85 kDa 
• Atom Count: 4,793 
• Modelled Residue Count: 567 
• Deposited Residue Count: 744 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex exonuclease RRP6	A, C, E	115	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: RRP6, UNC733, YOR001W EC: 3.1.13
UniProt
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12149  Go to UniProtKB:  Q12149

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex protein LRP1	B, D, F	133	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LRP1, RRP47, YC1D, YHR081W
UniProt
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38801  Go to UniProtKB:  P38801

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth B], I [auth C], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.224 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.397	α = 90
b = 98.397	β = 90
c = 208.018	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
Aimless	data scaling
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Schuch, B., Conti, E.

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Funding Organization	Location	Grant Number
European Research Council		Advanced Investigator Grant 294371
Marie Curie		ITN RNPnet
German Research Foundation	Germany	SFB646, SFB1035, GRK1721, FOR1680, CIPSM

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Database references
• Version 2.0: 2017-09-06
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations, Refinement description