Scientists map kinesin-2 tail structure to understand cargo binding

For decades, scientists have known that motor proteins like kinesin-2 ferry vital cargo along microtubule "highways" inside cells. But how these molecular vehicles identify and bind to the right cargo remained a mystery. The new study provides a key piece of this puzzle by revealing the atomic-level structure of the kinesin-2 tail and its interaction with cargo and adaptor proteins.

This study, led by Professor Nobutaka Hirokawa from Juntendo University with Dr. Masahide Kikkawa from the University of Tokyo, Dr. Xuguang Jiang, a JSPS Postdoctoral Fellow, Dr. Radostin Danev from the University of Tokyo, and Mr. Sotaro Ichinose from Gunma University, was published in Science Advances on October 24, 2025.

Using cryo-electron microscopy and molecular dynamics simulations, the scientists reconstructed the structure of the heterotrimeric kinesin-2 complex (KIF3A/KIF3B/KAP3) bound to the cargo protein, adenomatous polyposis coli (APC). They discovered a unique structural motif in the tail region of KIF3A and KIF3B (termed hook-like adaptor and cargo-binding (HAC) domain) that acts as a molecular "hook," enabling the motor to assemble its adaptors and recognize cargo with high specificity.

Our study has uncovered a previously unknown 'hook-like' structural element, the HAC domain, in the tail of the motor protein kinesin-2. This domain acts as a molecular 'connector' that allows the motor to correctly recognize and transport its cargo inside cells."

Nobutaka Hirokawa, Professor, Juntendo University

The HAC domain consists of a helix–β-hairpin–helix (H-βh-H) motif that forms a scaffold for the adaptor protein KAP3 and the cargo protein APC. The study revealed four distinct binding interfaces between KIF3 and KAP3, with KIF3A playing a dominant role in cargo recognition. The researchers also found that the HAC/KAP3 structure resembles cargo-binding architectures of other motor proteins, such as dynein and kinesin-1, suggesting a shared recognition framework.

"This discovery builds on decades of research from our laboratory, which first identified and characterized the complete family of mammalian kinesin motor proteins in the 1980s and 1990s and later revealed how these molecular 'vehicles' move along the cytoskeletal 'highways' of the cell," Prof. Hirokawa said. "While we have long understood how these motors travel, the remaining mystery was how they know what to carry. Our new findings provide the first atomic-level insight into this 'logistics code' of cellular transport, the molecular rules that allow each motor to recognize and deliver its specific cargo with remarkable precision."

The team validated their structural model using cross-linking mass spectrometry, biochemistry, and neuronal cell biology. They showed that the HAC domain binds specifically to the ARM repeat region of APC, a tumor suppressor protein involved in neuronal RNA transport. Notably, KIF3A contributed the majority of the binding energy, while KIF3B played a structural support role.

"Defects in intracellular transport are linked to a variety of human diseases, including neurodegenerative diseases, neurodevelopmental disorders, and ciliopathies," Prof. Hirokawa said. "Understanding how motor proteins accurately recognize and deliver their cargo provides a molecular basis for developing new diagnostic and therapeutic approaches."

The study also highlights the potential for drug discovery targeting motor-cargo interactions and the design of artificial transport systems that mimic biological logistics. However, the authors note that some regions of the protein complex remain unresolved due to structural flexibility, and further studies are needed to explore cargo diversity and regulatory mechanisms. This research marks a major step toward decoding the cellular transport system and understanding motor-driven cargo delivery in neurons.