6C90

Human Mtr4 helicase in complex with ZCCHC8-CTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for MTR4-ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex.

Puno, M.R.Lima, C.D.

(2018) Proc Natl Acad Sci U S A 115: E5506-E5515

  • DOI: 10.1073/pnas.1803530115
  • Primary Citation of Related Structures:  
    6C90

  • PubMed Abstract: 
  • The nuclear exosome-targeting (NEXT) complex functions as an RNA exosome cofactor and is involved in surveillance and turnover of aberrant transcripts and noncoding RNAs. NEXT is a ternary complex composed of the RNA-binding protein RBM7, the scaffold zinc-knuckle protein ZCCHC8, and the helicase MTR4 ...

    The nuclear exosome-targeting (NEXT) complex functions as an RNA exosome cofactor and is involved in surveillance and turnover of aberrant transcripts and noncoding RNAs. NEXT is a ternary complex composed of the RNA-binding protein RBM7, the scaffold zinc-knuckle protein ZCCHC8, and the helicase MTR4. While RNA interactions with RBM7 are known, it remains unclear how NEXT subunits collaborate to recognize and prepare substrates for degradation. Here, we show that MTR4 helicase activity is enhanced when associated with RBM7 and ZCCHC8. While uridine-rich substrates interact with RBM7 and are preferred, optimal activity is observed when substrates include a polyadenylated 3' end. We identify a bipartite interaction of ZCCHC8 with MTR4 and uncover a role for the conserved C-terminal domain of ZCCHC8 in stimulating MTR4 helicase and ATPase activities. A crystal structure reveals that the ZCCHC8 C-terminal domain binds the helicase core in a manner that is distinct from that observed for Saccharomyces cerevisiae exosome cofactors Trf4p and Air2p. Our results are consistent with a model whereby effective targeting of substrates by NEXT entails recognition of elements within the substrate and activation of MTR4 helicase activity.


    Organizational Affiliation

    Howard Hughes Medical Institute, Sloan Kettering Institute, New York, NY 10065.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome RNA helicase MTR4,Exosome RNA helicase MTR4 A734Homo sapiensMutation(s): 0 
Gene Names: MTREXDOB1KIAA0052MTR4SKIV2L2
EC: 3.6.4.13
Find proteins for P42285 (Homo sapiens)
Explore P42285 
Go to UniProtKB:  P42285
NIH Common Fund Data Resources
PHAROS:  P42285
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger CCHC domain-containing protein 8 B52Homo sapiensMutation(s): 0 
Gene Names: ZCCHC8
Find proteins for Q6NZY4 (Homo sapiens)
Explore Q6NZY4 
Go to UniProtKB:  Q6NZY4
NIH Common Fund Data Resources
PHAROS:  Q6NZY4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.635α = 90
b = 147.635β = 90
c = 101.589γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-25 
  • Released Date: 2018-05-30 
  • Deposition Author(s): Puno, M.R., Lima, C.D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118080
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence