8ZH9 | pdb_00008zh9

The structure of ELK1-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb8ZH9/pdb
• NAKB: 8ZH9

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Sus scrofa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-10 Released: 2025-05-21 
• Deposition Author(s): Liu, G., Sun, L.T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Host genetic variation governs PCV2 susceptibility through CXCL13 and ELK1-mediated immune regulation.

Liu, G., Gao, Y., Cheng, Y., Wang, W., Li, X., Wu, Y., Gao, F., Zhou, Z.W., Sun, Y., Jiang, Y., Yang, N., Shu, Y., Sun, L.

(2025) Int J Biol Macromol 310: 143170-143170

• PubMed: 40267997 
• DOI: https://doi.org/10.1016/j.ijbiomac.2025.143170
• Primary Citation of Related Structures:  
  8ZH9


• PubMed Abstract: 
  

  Pathogenic viruses can drive evolutionary adaptations in host biology, leading to diversified immune responses and variable susceptibility among individuals. This study examined how genetic variation in host regulatory regions impacts susceptibility to viral infections. Utilizing a porcine model, we identified the single nucleotide polymorphism (SNP) g.-1014G>A as a critical determinant of CXCL13 expression levels following PCV2 viral exposure. Structural analyses showed that the transcription factor ELK1 specifically recognized and bound to the g.-1014G allele, but not to the g.-1014A allele, through essential residues such as Arg65. This allele-specific binding led to differential CXCL13 expression, with the G allele associated with increased resistance to viral infection. Functional studies demonstrated that CXCL13 played a multifaceted role in antiviral immunity, including the inhibition of viral replication, modulation of immune-related pathways, and attenuation of virus-induced apoptosis. The CXCL13-mediated response involved the activation of the PI3K/Akt pathway, enhancing cell survival during viral challenges. This SNP-dependent regulation of a host factor represented a novel mechanism underlying genetic differences in viral susceptibility, with potential implications for developing broadly applicable antiviral strategies.

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Organizational Affiliation: 
• Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China.
Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences (CAS), Tianjin 300308, China.
Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China. Electronic address: [e-mail].
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: [e-mail].
Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100176, China. Electronic address: [e-mail].
Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: mass spectrometry, gel filtration

Macromolecule Content 

• Total Structure Weight: 20.86 kDa 
• Atom Count: 1,412 
• Modeled Residue Count: 118 
• Deposited Residue Count: 126 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ETS transcription factor ELK1	C	94	Sus scrofa	Mutation(s): 0  Gene Names: ELK1
UniProt
Find proteins for A0A5G2QTN4 (Sus scrofa) Explore A0A5G2QTN4  Go to UniProtKB:  A0A5G2QTN4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*CP*AP*GP*TP*CP*CP*GP*GP*AP*AP*AP*TP*TP*T)-3')	A	16	Sus scrofa

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*TP*TP*TP*CP*CP*GP*GP*AP*CP*TP*GP*GP*T)-3')	B	16	Sus scrofa

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.318	α = 90
b = 62.345	β = 90
c = 99.011	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Liu, G., Sun, L.T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271314
National Natural Science Foundation of China (NSFC)	China	32102504

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 1.1: 2025-07-23
  Changes: Database references