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 9ZEB | pdb_00009zeb

Cryo-EM structure of the TREX-2.1 complex (Thp3/Csn12/Sem1) bound to the DEAD-box ATPase Sub2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9ZEB

This is version 1.0 of the entry. See complete history. 

Literature

Conserved mRNP remodeling mechanism of the TREX-2.1 complex.

Angelos, A.E., Asada, R., Clarke, B.P., Hill, P.S., Li, L., Mei, M., Smith, J.L., Xie, E.R., Reter, W.C., Smithee, S.J., Xie, Y., Montpetit, B., Ren, Y.

(2026) Nucleic Acids Res 54

  • DOI: https://doi.org/10.1093/nar/gkag884
  • Primary Citation Related Structures: 
    9ZEB

  • PubMed Abstract: 

    Processing, packaging, and nuclear export of messenger ribonucleoprotein particles (mRNPs) are critical for eukaryotic gene expression, with the DEAD-box ATPase DDX39B (yeast Sub2) playing a central role in mRNP processing and remodeling. Our recent studies identified human TREX-2 (GANP•PCID2•DSS1), yeast TREX-2 (Sac3•Thp1•Sem1), and a related human TREX-2.1 complex (LENG8•PCID2•DSS1) as key regulators of DDX39B/Sub2. Here, we characterize the yeast TREX-2.1 (scTREX-2.1) complex, composed of Thp3, Csn12, and Sem1. We show that the scTREX-2.1 complex directly interacts with Sub2 and co-occupies a fraction of CBC-containing mRNPs with Sub2. Using cryo-electron microscopy , we determined the structure of scTREX-2.1 bound to Sub2, revealing a conserved "trigger loop" mechanism by which scTREX-2.1 regulates Sub2 activity. Functional assays show that disruption of scTREX-2.1 leads to the accumulation of intron-containing pre-mRNAs. These findings uncover a conserved mechanism from yeast to humans by which TREX-2 and TREX-2.1 complexes regulate Sub2/DDX39B during nuclear mRNP maturation, providing insights into the coordination of mRNP remodeling and processing prior to nuclear export.


  • Organizational Affiliation: 
    • Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States.

Macromolecule Content 

  • Total Structure Weight: 151.51 kDa 
  • Atom Count: 7,777 
  • Modeled Residue Count: 946 
  • Deposited Residue Count: 1,309 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein THP3336Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: THP3, YPR045C, YP9499.03c
UniProt
Find proteins for Q12049 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12049 
Go to UniProtKB:  Q12049
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12049
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cop9 signalosome complex subunit 12429Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CSN12, YJR084W, J1860
UniProt
Find proteins for P47130 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47130 
Go to UniProtKB:  P47130
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UniProt GroupP47130
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM193Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEM1, DSH1, YDR363W-A
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
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase SUB2451Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: SUB2, YDL084W
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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
E [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
A1AMM
Query on A1AMM
D
L-PEPTIDE LINKINGC16 H17 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release