29ZF
Crystal structure of human NIF3L1 protein with trimer in ASU
Summary for 29ZF
| Entry DOI | 10.2210/pdb29zf/pdb |
| Descriptor | NIF3-like protein 1, ZINC ION (3 entities in total) |
| Functional Keywords | duf34, nif3, nif3l1, protein of unknown function, metal binding protein |
| Biological source | Homo sapiens (human) |
| Total number of polymer chains | 3 |
| Total formula weight | 122849.43 |
| Authors | Wator-Wilk, E.,Wilk, P.,Zak, K.M.,Grudnik, P. (deposition date: 2026-04-15, release date: 2026-09-23) |
| Primary citation | Wator-Wilk, E.,Zak, K.,Wilk, P.,Kochanowski, P.,Maslanka, A.,Skalniak, L.,Grudnik, P. Crystal structure of human NIF3-like protein reveals dynamic hexameric assembly with a single divalent metal binding site. Febs J., 2026 Cited by PubMed Abstract: NIF3L1 (also NIF3) is a highly conserved protein belonging to the DUF34 protein family with unknown molecular function, present in bacteria, archaea, and eukaryotes. Here, we present the first crystal structures of human NIF3, revealing a hexameric toroidal assembly with a central cavity gated by PII-like insertion domains. Each subunit contains a mononuclear zinc-binding site, marking a clear departure from the dinuclear metal centers of bacterial homologs and potential functional divergence of the scaffold. We further capture a half-capped state with asymmetric disorder of the insertion domains and local rearrangements near the metal site, suggesting a gating mechanism that regulates access to the internal chamber. These findings uncover an unexpected level of structural plasticity in human NIF3 and provide a framework for future studies investigating whether the different lid conformations observed in our structures have functional relevance in vivo. PubMed: 42741873DOI: 10.1111/febs.70724 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.27 Å) |
Structure validation
No wwPDB Validation report is currently available for this entry.
