9VJL | pdb_00009vjl

Phosphorylation dependent recognition of RIPK1 by phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1

• PDB DOI: https://doi.org/10.2210/pdb9VJL/pdb
• BMRB: 36768

• Classification: APOPTOSIS
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-20 Released: 2026-03-25 
• Deposition Author(s): Liu, J., Liu, Z., Xue, H., Xie, X., Sun, W., Chou, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Repression of RIPK1 kinase by INPP5D inhibits expression of diverse proinflammatory mediators and late-onset Alzheimer's disease risk factors.

Xie, X., Liu, J., Liang, W., Zhang, Y., Gong, X., Yuan, S., Qi, C., Huang, M., Shi, L., Hou, M., Zhang, M., Liu, W., Sun, W., Wu, Y., Li, C., Cao, Z., Jing, H., Qian, L., Liu, J., Yuan, S., Wang, Q., Shen, Y., Liu, Z., Li, Y., Pan, H., Zhu, B., Shan, B., He, K., Wang, W., Zou, C., Li, Y., Chou, J.J., Yuan, J.

(2026) Immunity 59: 419-437.e11

• PubMed: 41633359 
• DOI: https://doi.org/10.1016/j.immuni.2026.01.014
• Primary Citation Related Structures: 
  9VJL


• PubMed Abstract: 
  

  Genome-wide association studies strongly implicate neuroinflammation in late-onset Alzheimer's disease (LOAD). Genetic risk loci for LOAD are enriched for genes expressed in microglia, but the relationship among microglial LOAD risk genes has been unclear. We found that the N-terminal SH2 domain of INPP5D, an important LOAD risk gene, directly interacted with the cell death regulator RIPK1 at p-Y383 to suppress RIPK1 kinase activation. Microglial INPP5D deficiency cell-autonomously promoted RIPK1-mediated transcriptional induction of diverse LOAD risk genes, proinflammatory cytokines, complements, and ROS mediators, as well as proinflammatory signaling mediators such as Toll-like receptors (TLRs), MyD88, Nlrp3, gasdermin D, and Zbp1. RIPK1-regulated microglial transcriptomic signatures were found in microglial subtypes implicated in human Alzheimer's disease (AD) pathogenesis. Furthermore, microglial INPP5D deficiency promoted aging-dependent RIPK1-mediated development of neuronal TDP-43 pathology, neuronal loss, and motor dysfunction in a non-cell-autonomous manner. Our data suggest that INPP5D functions as an intracellular rheostat in regulating RIPK1-mediated neuroinflammation for promoting aging-related neurodegenerative diseases, including LOAD and AD-amyotrophic lateral sclerosis comorbidity.

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Organizational Affiliation: 
• Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201203, China.
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201203, China.
School of Life Sciences, Fudan University, Shanghai 200438, China.
School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; Nankai University, Tianjin, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201203, China.
Lingang Laboratory, Shanghai 200031, China.
Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University, Shanghai 200092, China.
Department of Neurology, Institute on Aging and Brain Disorders, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.
National Facility for Protein Science, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China.
Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China; Department of Neurology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China.
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China.
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201203, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 13.96 kDa 
• Atom Count: 983 
• Modeled Residue Count: 122 
• Deposited Residue Count: 122 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1	A	106	Mus musculus	Mutation(s): 0  Gene Names: Inpp5d, 7a33, Ship, Ship1 EC: 3.1.3.86 (PDB Primary Data), 3.1.3.56 (PDB Primary Data), 3.1.3.36 (PDB Primary Data)
UniProt
Find proteins for Q9ES52 (Mus musculus) Explore Q9ES52  Go to UniProtKB:  Q9ES52

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	B	16	Mus musculus	Mutation(s): 0  EC: 2.7.11.1
UniProt
Find proteins for Q60855 (Mus musculus) Explore Q60855  Go to UniProtKB:  Q60855

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Liu, J., Liu, Z., Xue, H., Xie, X., Sun, W., Chou, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release