5OKZ

Crystal Strucrure of the Mpp6 Exosome complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20004 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase.

Falk, S.Bonneau, F.Ebert, J.Kogel, A.Conti, E.

(2017) Cell Rep 20: 2279-2286

  • DOI: 10.1016/j.celrep.2017.08.033

  • PubMed Abstract: 
  • The RNA-degrading exosome mediates the processing and decay of many cellular transcripts. In the yeast nucleus, the ubiquitous 10-subunit exosome core complex (Exo-9-Rrp44) functions with four conserved cofactors (Rrp6, Rrp47, Mtr4, and Mpp6). Bioche ...

    The RNA-degrading exosome mediates the processing and decay of many cellular transcripts. In the yeast nucleus, the ubiquitous 10-subunit exosome core complex (Exo-9-Rrp44) functions with four conserved cofactors (Rrp6, Rrp47, Mtr4, and Mpp6). Biochemical and structural studies to date have shed insights into the mechanisms of the exosome core and its nuclear cofactors, with the exception of Mpp6. We report the 3.2-Å resolution crystal structure of a S. cerevisiae Exo-9-Mpp6 complex, revealing how linear motifs in the Mpp6 middle domain bind Rrp40 via evolutionary conserved residues. In particular, Mpp6 binds near a tryptophan residue of Rrp40 that is mutated in human patients suffering from pontocerebellar hypoplasia. Using biochemical assays, we show that Mpp6 is required for the ability of Mtr4 to extend the trajectory of an RNA entering the exosome core, suggesting that it promotes the channeling of substrates from the nuclear helicase to the processive RNase.


    Organizational Affiliation

    Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152 Martinsried/Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component CSL4
m, I, S, c
295Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CSL4 (SKI4)
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53859
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP45
A, K, U, e
305Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP45
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05636
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component SKI6
B, L, V, f
249Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKI6 (ECM20, RRP41)
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46948
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP43
C, M, W, g
394Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP43
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25359
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP46
D, N, X, h
226Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP46
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53256
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP42
E, O, Y, i
268Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP42
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12277
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component MTR3
F, P, Z, j
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MTR3
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48240
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP40
G, Q, a, k
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP40
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08285
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP4
H, R, b, l
316Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP4
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38792
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
M-phase phosphoprotein 6 homolog
J, T, d, n
190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MPP6
Find proteins for P53725 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MPP6
Go to UniProtKB:  P53725
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
b, f, G, H, l, R
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
g, O
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TAM
Query on TAM

Download SDF File 
Download CCD File 
A, e, K, U
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20004 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 161.779α = 90.00
b = 237.430β = 110.37
c = 201.895γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata reduction
DIALSdata processing
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium294371
German Research FoundationGermanySFB1035
German Research FoundationGermanyGRK1721
German Research FoundationGermanyCluster of Excellence CIPSM

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references