4XFS

Structure of IL-18 SER Mutant I

• PDB DOI: https://doi.org/10.2210/pdb4XFS/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-12-28 Released: 2015-06-10 
• Deposition Author(s): Krumm, B.E., Meng, X., Xiang, Y., Deng, J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Oklahoma State University

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.229 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Literature

Crystallization of interleukin-18 for structure-based inhibitor design.

Krumm, B., Meng, X., Xiang, Y., Deng, J.

(2015) Acta Crystallogr F Struct Biol Commun 71: 710-717

• PubMed: 26057800 
• DOI: https://doi.org/10.1107/S2053230X15006871
• Primary Citation of Related Structures:  
  4XFS, 4XFT, 4XFU


• PubMed Abstract: 
  

  Interleukin-18 (IL-18) is a pleiotropic pro-inflammatory cytokine belonging to the IL-1 superfamily. IL-18 plays an important role in host innate and acquired immune defense, with its activity being modulated in vivo by its naturally occurring antagonist IL-18 binding protein (IL-18BP). Recent crystal structures of human IL-18 (hIL-18) in complex with its antagonist or cognate receptor(s) have revealed a conserved binding interface on hIL-18 representing a promising drug target. An important step in this process is obtaining crystals of apo hIL-18 or hIL-18 in complex with small-molecule inhibitors, preferably under low ionic strength conditions. In this study, surface-entropy reduction (SER) and rational protein design were employed to facilitate the crystallization of hIL-18. The results provide an excellent platform for structure-based drug design.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

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: 36.51 kDa 
• Atom Count: 2,642 
• Modelled Residue Count: 313 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-18	A, B	157	Homo sapiens	Mutation(s): 5  Gene Names: IL18, IGIF, IL1F4
UniProt & NIH Common Fund Data Resources
Find proteins for Q14116 (Homo sapiens) Explore Q14116  Go to UniProtKB:  Q14116
PHAROS:  Q14116 GTEx:  ENSG00000150782

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.229 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.982	α = 77.8
b = 42.258	β = 83.63
c = 52.343	γ = 67.13

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Krumm, B.E., Meng, X., Xiang, Y., Deng, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI113539
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI079217
Oklahoma State University	United States	OKL02848

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2015-07-01
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Advisory, Data collection, Database references, Refinement description