8U8C | pdb_00008u8c

Crystal structure of the TREX-2 complex in complex with the N-terminal motif of Sub2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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Literature

Structures and mRNP remodeling mechanism of the TREX-2 complex.

Xie, Y.Clarke, B.P.Xie, D.Mei, M.Bhat, P.Hill, P.S.Angelos, A.E.Cagatay, T.Haider, M.Collier, S.E.Chambers, M.G.Aksenova, V.Dasso, M.Fontoura, B.M.A.Ren, Y.

(2025) Structure 33: 566-582.e6

  • DOI: https://doi.org/10.1016/j.str.2024.12.019
  • Primary Citation of Related Structures:  
    8U8C, 8U8D, 8U8E

  • PubMed Abstract: 

    mRNAs are packaged with proteins into messenger ribonucleoprotein complexes (mRNPs) in the nucleus. mRNP assembly and export are of fundamental importance for all eukaryotic gene expression. Before export to the cytoplasm, mRNPs undergo dynamic remodeling governed by the DEAD-box helicase DDX39B (yeast Sub2). DDX39B/Sub2 primarily functions in the nucleus and leaves the mRNP prior to export through the nuclear pore complex; however, the underlying mechanisms remain elusive. Here, we identify the conserved TREX-2 complex as the long-sought factor that facilitates DDX39B/Sub2 to complete the mRNP remodeling cycle. Our crystallographic and cryoelectron microscopy (cryo-EM) analyses demonstrate that TREX-2 modulates the activities of DDX39B/Sub2 through multiple interactions. Critically, a conserved "trigger loop" from TREX-2 splits the two RecA domains of DDX39B/Sub2 and promotes the removal of DDX39B/Sub2 from mRNP. Our findings suggest that TREX-2 coordinates with DDX39B/Sub2 and the human export receptor NXF1-NXT1 (yeast Mex67-Mtr2) to complete the final steps of nuclear mRNP assembly.


  • Organizational Affiliation
    • Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA. Electronic address: yihu.xie@vanderbilt.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear mRNA export protein SAC3497Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAC3
UniProt
Find proteins for P46674 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46674 
Go to UniProtKB:  P46674
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46674
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear mRNA export protein THP1455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: THP1
UniProt
Find proteins for Q08231 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08231 
Go to UniProtKB:  Q08231
Entity Groups  
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UniProt GroupQ08231
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEM1
UniProt
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O94742 
Go to UniProtKB:  O94742
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UniProt GroupO94742
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase SUB255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUB2
EC: 3.6.4.13
UniProt
Find proteins for Q07478 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07478 
Go to UniProtKB:  Q07478
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UniProt GroupQ07478
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.861α = 90
b = 87.001β = 90
c = 169.802γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133743

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references