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TitleStructural mechanism of DDX39B regulation by human TREX-2 and a related complex in mRNP remodeling.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 5471, Year 2025
Publish dateJul 1, 2025
AuthorsBradley P Clarke / Shengyan Gao / Menghan Mei / Dongqi Xie / Alexia E Angelos / Ashley Vazhavilla / Pate S Hill / Tolga Cagatay / Kimberly Batten / Jerry W Shay / Yihu Xie / Beatriz M A Fontoura / Yi Ren /
PubMed AbstractNuclear export of mRNAs in the form of messenger ribonucleoprotein particles (mRNPs) is an obligatory step for eukaryotic gene expression. The DEAD-box ATPase DDX39B (also known as UAP56) is a ...Nuclear export of mRNAs in the form of messenger ribonucleoprotein particles (mRNPs) is an obligatory step for eukaryotic gene expression. The DEAD-box ATPase DDX39B (also known as UAP56) is a multifunctional regulator of nuclear mRNPs. How DDX39B mediates mRNP assembly and export in a controlled manner remains elusive. Here, we identify a novel complex TREX-2.1 localized in the nucleus that facilitates the release of DDX39B from the mRNP. TREX-2.1 is composed of three subunits, LENG8, PCID2, and DSS1, and shares the latter two subunits with the nuclear pore complex-associated TREX-2 complex. Cryo-EM structures of TREX-2.1/DDX39B and TREX-2/DDX39B identify a conserved trigger loop in the LENG8 and GANP subunit of the respective TREX-2.1 and TREX-2 complex that is critical for DDX39B regulation. RNA sequencing from LENG8 knockdown cells shows that LENG8 influences the nucleocytoplasmic ratio of a subset of mRNAs with high GC content. Together, our findings lead to a mechanistic understanding of the functional cycle of DDX39B and its regulation by TREX-2 and TREX-2.1 in mRNP processing.
External linksNat Commun / PubMed:40595470 / PubMed Central
MethodsEM (single particle)
Resolution2.79 - 3.28 Å
Structure data

EMDB-46981: Cryo-EM map of human TREX-2 complex bound to full-length DDX39B
Method: EM (single particle) / Resolution: 3.25 Å

46982

9dlp

EMDB-46982, PDB-9dlp:
Cryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56)
Method: EM (single particle) / Resolution: 2.79 Å

46983

9dlr

EMDB-46983, PDB-9dlr:
Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to the N-terminal motif of DDX39B(UAP56)
Method: EM (single particle) / Resolution: 3.08 Å

46985

9dlv

EMDB-46985, PDB-9dlv:
Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to DDX39B(UAP56)
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-47126: Cryo-EM map of the human TREX-2.1 complex bound to DDX39B(UAP56)
Method: EM (single particle) / Resolution: 3.28 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
KeywordsRNA BINDING PROTEIN / mRNA nuclear export / TREX / TREX-2 / UAP56 / DDX39B / RNA BINDING PROTEIN/Hydrolase / LENG8 / RNA BINDING PROTEIN-Hydrolase complex

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