4LNQ

Crystal structure of Ifi202 HINa domain in complex with 20bp dsDNA

• PDB DOI:  https://doi.org/10.2210/pdb4LNQ/pdb
• NAKB: 4LNQ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-07-12 Released: 2014-01-08 
• Deposition Author(s): Li, H., Wang, Z.-X., Wu, J.-W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Structural mechanism of DNA recognition by the p202 HINa domain: insights into the inhibition of Aim2-mediated inflammatory signalling.

Li, H., Wang, J., Wang, J., Cao, L.S., Wang, Z.X., Wu, J.W.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 21-29

• PubMed: 24419611 
• DOI: https://doi.org/10.1107/S2053230X1303135X
• Primary Citation of Related Structures:  
  4LNQ


• PubMed Abstract: 
  

The HIN-200 family of proteins play significant roles in inflammation-related processes. Among them, AIM2 (absent in melanoma 2) and IFI16 (γ-interferon-inducible protein 16) recognize double-stranded DNA to initiate inflammatory responses. In contrast, p202, a mouse interferon-inducible protein containing two HIN domains (HINa and HINb), has been reported to inhibit Aim2-mediated inflammatory signalling in mouse. To understand the inhibitory mechanism, the crystal structure of the p202 HINa domain in complex with a 20 bp DNA was determined, in which p202 HINa nonspecifically recognizes both strands of DNA through electrostatic attraction. The p202 HINa domain binds DNA more tightly than does AIM2 HIN, and the DNA-binding mode of p202 HINa is different from that of the AIM2 HIN and IFI16 HINb domains. These results, together with the reported data on p202 HINb, lead to an interaction model for full-length p202 and dsDNA which provides a conceivable mechanism for the negative regulation of Aim2 inflammasome activation by p202.

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Organizational Affiliation: 

MOE Key Laboratory of Protein Science and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 57.46 kDa 
• Atom Count: 4,264 
• Modelled Residue Count: 427 
• Deposited Residue Count: 434 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-activable protein 202	A, B	197	Mus musculus	Mutation(s): 4  Gene Names: Ifi202, Ifi202a, Ifi202b
UniProt
Find proteins for Q9R002 (Mus musculus) Explore Q9R002  Go to UniProtKB:  Q9R002

Entity ID: 2
Molecule	Chains	Length	Organism	Image
20bp DNA	C, D	20	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.353	α = 90
b = 105.566	β = 90
c = 65.143	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-08 
Deposition Author(s): Li, H., Wang, Z.-X., Wu, J.-W.

Revision History  

• Version 1.0: 2014-01-08
  Type: Initial release
  
• Version 1.1: 2014-02-12
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description