Integrative structural analysis of the human nuclear pore complex reveals that the TREX-2 mRNA export complex components GANP, Centrin-2, and ENY2 are integral structural components of the nuclear ring rather than transiently associated factors, and identifies five previously unrecognized nucleoporins (TMEM209, SMPD4, GANP, Centrin-2, ENY2) that establish two spatially distinct mRNA export platforms—TREX-2 at the nuclear entrance and NUP214 at the cytoplasmic exit—positioned at opposite ends of the central transport channel to coordinate sequential mRNP remodeling during nuclear export.

Nuclear pore complexes (NPCs) control nucleocytoplasmic transport in eukaryotes, yet their architecture remains incompletely understood. Here we report a substantially extended structure of the human NPC, obtained by combining cryo-electron tomography, crosslinking mass spectrometry, and AI-assisted integrative modeling. We resolve the molecular arrangement of TPR, NUP153, NUP50 and ZC3HC1, and reveal that five additional proteins — TMEM209, SMPD4, GANP, Centrin-2 and ENY2 — are incorporated into the NPC. Unexpectedly, GANP, Centrin-2 and ENY2, core members of the TREX-2 mRNA export complex, are built into the nuclear ring. This finding establishes TREX-2 not as a transiently associated factor, but as an integral NPC module, positioning it opposite of the cytoplasmic NUP214 mRNA export platform. Together, our results redefine the molecular composition of the inner ring, nuclear ring and nuclear basket. They suggest a direct structural basis that couples TREX-2-mediated mRNP remodeling to NPC-facilitated transport.