6IEH

Crystal structures of the hMTR4-NRDE2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction.

Wang, J.Chen, J.Wu, G.Zhang, H.Du, X.Chen, S.Zhang, L.Wang, K.Fan, J.Gao, S.Wu, X.Zhang, S.Kuai, B.Zhao, P.Chi, B.Wang, L.Li, G.Wong, C.C.L.Zhou, Y.Li, J.Yun, C.Cheng, H.

(2019) Genes Dev 33: 536-549

  • DOI: https://doi.org/10.1101/gad.322602.118
  • Primary Citation of Related Structures:  
    6IEG, 6IEH

  • PubMed Abstract: 

    The exosome functions in the degradation of diverse RNA species, yet how it is negatively regulated remains largely unknown. Here, we show that NRDE2 forms a 1:1 complex with MTR4, a nuclear exosome cofactor critical for exosome recruitment, via a conserved MTR4-interacting domain (MID). Unexpectedly, NRDE2 mainly localizes in nuclear speckles, where it inhibits MTR4 recruitment and RNA degradation, and thereby ensures efficient mRNA nuclear export. Structural and biochemical data revealed that NRDE2 interacts with MTR4's key residues, locks MTR4 in a closed conformation, and inhibits MTR4 interaction with the exosome as well as proteins important for MTR4 recruitment, such as the cap-binding complex (CBC) and ZFC3H1. Functionally, MID deletion results in the loss of self-renewal of mouse embryonic stem cells. Together, our data pinpoint NRDE2 as a nuclear exosome negative regulator that ensures mRNA stability and nuclear export.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome RNA helicase MTR4A [auth B]979Homo sapiensMutation(s): 0 
Gene Names: MTREXDOB1KIAA0052MTR4SKIV2L2
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P42285 (Homo sapiens)
Explore P42285 
Go to UniProtKB:  P42285
PHAROS:  P42285
GTEx:  ENSG00000039123 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42285
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NRDE2 homologB [auth A]105Homo sapiensMutation(s): 0 
Gene Names: NRDE2C14orf102
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7Z3 (Homo sapiens)
Explore Q9H7Z3 
Go to UniProtKB:  Q9H7Z3
PHAROS:  Q9H7Z3
GTEx:  ENSG00000119720 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7Z3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.305α = 90
b = 113.728β = 96.49
c = 80.717γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description