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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1101/gad.322602.118
  • Structures With Same Primary Citation

  • 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 co ...

    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

    Shanghai Key Laboratory of Molecular Andrology, 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome RNA helicase MTR4B979Homo 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: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein NRDE2 homologA105Homo sapiensMutation(s): 0 
Gene Names: NRDE2C14orf102
Find proteins for Q9H7Z3 (Homo sapiens)
Explore Q9H7Z3 
Go to UniProtKB:  Q9H7Z3
NIH Common Fund Data Resources
PHAROS  Q9H7Z3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-09-14 
  • Released Date: 2019-04-03 
  • Deposition Author(s): Chen, J.Y., Yun, C.H.

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references