Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain–side-chain interactions across protein–protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein–protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.

蛋白质结晶在结构生物学中起着核心作用。尽管如此，人们对结晶过程仍然知之甚少，而且高度依赖经验，晶体接触、晶格堆积排列和空间群偏好在很大程度上是不可预测的。通过精确设计的跨蛋白质-蛋白质界面的侧链-侧链相互作用来编程蛋白质结晶是一个巨大的挑战。在这里，我们开发了一种通用的计算方法，用于设计具有原子精度的预先指定的晶格结构的三维蛋白质晶体，该方法分层地限制了系统自由度的总数。我们设计了三对低聚物，它们可以单独纯化，并在混合后自发自组装成 >100 µm 的三维晶体。这些晶体的结构几乎与计算设计模型相同，在整体结构和特定的蛋白质-蛋白质相互作用方面密切对应。晶体晶胞的尺寸可以系统地重新设计，同时保留空间群对称性和整体结构，并且晶体极其多孔且高度稳定。我们的方法能够以高精度计算设计蛋白质晶体，并且设计的蛋白质晶体在其一级序列中编码有结构和组装信息，为生物材料工程提供了强大的平台。