8U8D | pdb_00008u8d

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear mRNA export factor497Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SAC3
UniProt
Find proteins for P46674 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P46674
Entity Groups  
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UniProt GroupP46674
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
THP1 isoform 1455Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: THP1
UniProt
Find proteins for Q08231 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q08231
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UniProt GroupQ08231
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM189Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEM1
UniProt
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupO94742
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicase446Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUB2GI527_G0000845
EC: 3.6.4.13
UniProt
Find proteins for Q07478 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q07478
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UniProt GroupQ07478
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PBF
Query on PBF
D
L-PEPTIDE LINKINGC16 H15 N O3PHE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Data collection, Database references