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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase.

Wasmuth, E.V.Zinder, J.C.Zattas, D.Das, M.Lima, C.D.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.29062

  • PubMed Abstract: 
  • Nuclear RNA exosomes catalyze a range of RNA processing and decay activities that are coordinated in part by cofactors, including Mpp6, Rrp47, and the Mtr4 RNA helicase. Mpp6 interacts with the nine-subunit exosome core, while Rrp47 stabilizes the ex ...

    Nuclear RNA exosomes catalyze a range of RNA processing and decay activities that are coordinated in part by cofactors, including Mpp6, Rrp47, and the Mtr4 RNA helicase. Mpp6 interacts with the nine-subunit exosome core, while Rrp47 stabilizes the exoribonuclease Rrp6 and recruits Mtr4, but it is less clear if these cofactors work together. Using biochemistry with Saccharomyces cerevisiae proteins, we show that Rrp47 and Mpp6 stimulate exosome-mediated RNA decay, albeit with unique dependencies on elements within the nuclear exosome. Mpp6-exosomes can recruit Mtr4, while Mpp6 and Rrp47 each contribute to Mtr4-dependent RNA decay, with maximal Mtr4-dependent decay observed with both cofactors. The 3.3 Å structure of a twelve-subunit nuclear Mpp6 exosome bound to RNA shows the central region of Mpp6 bound to the exosome core, positioning its Mtr4 recruitment domain next to Rrp6 and the exosome central channel. Genetic analysis reveals interactions that are largely consistent with our model.


    Organizational Affiliation

    Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP45
A
305Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRP45
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05636
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component SKI6
B
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SKI6 (ECM20, RRP41)
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46948
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP43
C
394Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRP43
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25359
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP46
D
225Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRP46
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53256
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP42
E
269Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRP42
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12277
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component MTR3
F
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: MTR3
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48240
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP40
G
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRP40
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08285
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP4
H
363Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRP4
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38792
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component CSL4
I
296Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CSL4 (SKI4)
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53859
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP6
J
559Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRP6 (UNC733)
EC: 3.1.13.-
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12149
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease DIS3
K
1003Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: DIS3 (RRP44)
EC: 3.1.13.-, 3.1.26.-
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: DIS3
Go to UniProtKB:  Q08162
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
M-phase phosphoprotein 6 homolog
L
42Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: MPP6
Find proteins for P53725 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MPP6
Go to UniProtKB:  P53725
Entity ID: 13
MoleculeChainsLengthOrganism
RNA (11-MER)M11Homo sapiens
Entity ID: 14
MoleculeChainsLengthOrganism
RNA (19-MER)N19Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, G, K
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, K
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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 = 141.090α = 90.00
b = 213.592β = 90.00
c = 225.909γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM079196
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35GM118080
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF31GM097910
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/National Cancer InstituteUnited StatesP30CA008748

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references