8ZU6 | pdb_00008zu6

Solution NMR Structure of PACT D3 Homodimer

• PDB DOI: https://doi.org/10.2210/pdb8ZU6/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-08 Released: 2025-04-16 
• Deposition Author(s): Zhao, L., Ahmad, S., Hur, S., Chou, J.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

PACT prevents aberrant activation of PKR by endogenous dsRNA without sequestration.

Ahmad, S., Zou, T., Hwang, J., Zhao, L., Wang, X., Davydenko, A., Buchumenski, I., Zhuang, P., Fishbein, A.R., Capcha-Rodriguez, D., Orgel, A., Levanon, E.Y., Myong, S., Chou, J., Meyerson, M., Hur, S.

(2025) Nat Commun 16: 3325-3325

• PubMed: 40199855 
• DOI: https://doi.org/10.1038/s41467-025-58433-x
• Primary Citation of Related Structures:  
  8ZU6


• PubMed Abstract: 
  

  The innate immune sensor PKR for double-stranded RNA (dsRNA) is critical for antiviral defense, but its aberrant activation by cellular dsRNA is linked to various diseases. The dsRNA-binding protein PACT plays a critical yet controversial role in this pathway. We show that PACT directly suppresses PKR activation by endogenous dsRNA ligands, such as inverted-repeat Alu RNAs, which robustly activate PKR in the absence of PACT. Instead of competing for dsRNA binding, PACT prevents PKR from scanning along dsRNA-a necessary step for PKR molecules to encounter and phosphorylate each other for activation. While PKR favors longer dsRNA for increased co-occupancy and scanning-mediated activation, longer dsRNA is also more susceptible to PACT-mediated regulation due to increased PACT-PKR co-occupancy. Unlike viral inhibitors that constitutively suppress PKR, this RNA-dependent mechanism allows PACT to fine-tune PKR activation based on dsRNA length and quantity, ensuring self-tolerance without sequestering most cellular dsRNA.

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Organizational Affiliation: 
• Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. [e-mail].
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China. [e-mail].
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. [e-mail].
Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA. [e-mail].
Department of Genetics, Harvard Medical School, Boston, MA, USA. [e-mail].
Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. [e-mail].
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 20.54 kDa 
• Atom Count: 1,060 
• Modeled Residue Count: 140 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-inducible double-stranded RNA-dependent protein kinase activator A	A, B	94	Homo sapiens	Mutation(s): 0  Gene Names: PRKRA, PACT, RAX, HSD-14, HSD14
UniProt & NIH Common Fund Data Resources
Find proteins for O75569 (Homo sapiens) Explore O75569  Go to UniProtKB:  O75569
PHAROS:  O75569 GTEx:  ENSG00000180228

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Zhao, L., Ahmad, S., Hur, S., Chou, J.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release