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<p>Protein complexes are fundamental to all biological processes. Public repositories have expanded to include millions of potential protein–protein interactions (PPIs) from human and diverse model organisms. Yet, large-scale structural characterization of these complexes—especially across different biological kingdoms—has lagged far behind, leaving most potential and unidentified interactions unresolved. Here, we present a comprehensive atlas of 1.1 million predicted protein–protein interaction structures generated with the AlphaFold2-based ColabFold framework. This dataset spans proteome-wide interactions from bacteria, archaea, humans, mice, plants, and human–virus pairs. Overall, we identify 181,671 high-confidence protein complex structures, especially 37,855 in the human interactome. Structural clustering revealed numerous conserved protein complex architectures shared across kingdoms, providing insights into previously uncharacterized biological functions. Supported by co-immunoprecipitation experiments, we further identify candidate viral receptors for <i>Human mastadenovirus A</i> and <i>Papiine alphaherpesvirus 2</i>. Comparative analyses integrating our complex structures with the AlphaFold monomeric structure database uncovered widespread gene fusion and fission events during evolution. Finally, we demonstrate how our dataset can enhance protein binding–surface prediction using deep learning approaches, illustrating its broad utility beyond structural modeling alone. Altogether, this atlas to our knowledge, represents one of the most extensive cross-kingdom resources and opens avenues for future discoveries in various biomedical applications.</p>

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Atlas of predicted protein complex structures across kingdoms

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年3月25日

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  • Xianzhi Qi,
  • Cheng Ye,
  • Jianqiang Liang,
  • Shimin Wen,
  • Yuanyuan Li,
  • Kai Ding,
  • Yongfu Hao,
  • Junjie Fei,
  • Weian Mao,
  • Liupeng Li,
  • Zhiyu Lin,
  • Yichong Shen,
  • Hongjie Zhu,
  • Yayun Hu,
  • Rui Zhang,
  • Pengli Ji,
  • Yafei Lu,
  • Bonan Liu,
  • Han Wang,
  • Yuxuan Chen,
  • Zhenguo Ma,
  • Peiyuan Yang,
  • Xinyu Xu,
  • Junlong Wu,
  • Youyuan Zhu,
  • Qiaosha Zou,
  • Wencheng Zhu,
  • Kelu Yao,
  • Shuya Li,
  • Hongyi Xin,
  • Daji Ergu,
  • Jianyang Zeng,
  • Zhi-Xiong Jim Xiao,
  • Chunhua Shen,
  • Ying Cai,
  • Yong Yi,
  • Dacheng Ma

摘要

Protein complexes are fundamental to all biological processes. Public repositories have expanded to include millions of potential protein–protein interactions (PPIs) from human and diverse model organisms. Yet, large-scale structural characterization of these complexes—especially across different biological kingdoms—has lagged far behind, leaving most potential and unidentified interactions unresolved. Here, we present a comprehensive atlas of 1.1 million predicted protein–protein interaction structures generated with the AlphaFold2-based ColabFold framework. This dataset spans proteome-wide interactions from bacteria, archaea, humans, mice, plants, and human–virus pairs. Overall, we identify 181,671 high-confidence protein complex structures, especially 37,855 in the human interactome. Structural clustering revealed numerous conserved protein complex architectures shared across kingdoms, providing insights into previously uncharacterized biological functions. Supported by co-immunoprecipitation experiments, we further identify candidate viral receptors for Human mastadenovirus A and Papiine alphaherpesvirus 2. Comparative analyses integrating our complex structures with the AlphaFold monomeric structure database uncovered widespread gene fusion and fission events during evolution. Finally, we demonstrate how our dataset can enhance protein binding–surface prediction using deep learning approaches, illustrating its broad utility beyond structural modeling alone. Altogether, this atlas to our knowledge, represents one of the most extensive cross-kingdom resources and opens avenues for future discoveries in various biomedical applications.