29ZH

Crystal structure of human NIF3L1 - half open hexamer

Summary for 29ZH

• Entry DOI: 10.2210/pdb29zh/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: 6
• Total formula weight: 245698.87

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

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: 42741873
DOI: 10.1111/febs.70724

Experimental method

X-RAY DIFFRACTION (3.5 Å)