4JBK | pdb_00004jbk

Molecular basis for abrogation of activation of pro-inflammatory cytokines

• PDB DOI: https://doi.org/10.2210/pdb4JBK/pdb
• NAKB: 4JBK

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-19 Released: 2013-06-26 
• Deposition Author(s): Ru, H., Ni, X., Crowley, C., Zhao, L., Ding, W., Hung, L.-W., Shaw, N., Cheng, G., Liu, Z.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 
  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structural basis for termination of AIM2-mediated signaling by p202

Ru, H., Ni, X., Zhao, L., Crowley, C., Ding, W., Hung, L.-W., Shaw, N., Cheng, G., Liu, Z.-J.

(2013) Cell Res 23: 855-858

• PubMed: 23567559 
• DOI: https://doi.org/10.1038/cr.2013.52
• Primary Citation Related Structures: 
  4JBJ, 4JBK, 4JBM

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 107.94 kDa 
• Atom Count: 7,235 
• Modeled Residue Count: 813 
• Deposited Residue Count: 848 
• 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, C, D	198	Mus musculus	Mutation(s): 0  Gene Names: Ifi202a
UniProt
Find proteins for Q9R002 (Mus musculus) Explore Q9R002  Go to UniProtKB:  Q9R002

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')	E, F, G, H	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free:  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.304	α = 90
b = 109.94	β = 120.03
c = 106.137	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Ru, H., Ni, X., Crowley, C., Zhao, L., Ding, W., Hung, L.-W., Shaw, N., Cheng, G., Liu, Z.-J.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description