Skip to main content

 5FB8 | pdb_00005fb8

Structure of Interleukin-16 bound to the 14.1 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.205 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5FB8

This is version 1.3 of the entry. See complete history. 

Literature

Structure of a Potential Therapeutic Antibody Bound to Interleukin-16 (IL-16): MECHANISTIC INSIGHTS AND NEW THERAPEUTIC OPPORTUNITIES.

Hall, G., Cullen, E., Sawmynaden, K., Arnold, J., Fox, S., Cowan, R., Muskett, F.W., Matthews, D., Merritt, A., Kettleborough, C., Cruikshank, W., Taylor, D., Bayliss, R., Carr, M.D.

(2016) J Biol Chem 291: 16840-16848

  • DOI: https://doi.org/10.1074/jbc.M115.709303
  • Primary Citation Related Structures: 
    5FB8

  • PubMed Abstract: 

    Interleukin-16 (IL-16) is reported to be a chemoattractant cytokine and modulator of T-cell activation, and has been proposed as a ligand for the co-receptor CD4. The secreted active form of IL-16 has been detected at sites of TH1-mediated inflammation, such as those seen in autoimmune diseases, ischemic reperfusion injury (IRI), and tissue transplant rejection. Neutralization of IL-16 recruitment to its receptor, using an anti-IL16 antibody, has been shown to significantly attenuate inflammation and disease pathology in IRI, as well as in some autoimmune diseases. The 14.1 antibody is a monoclonal anti-IL-16 antibody, which when incubated with CD4(+) cells is reported to cause a reduction in the TH1-type inflammatory response. Secreted IL-16 contains a characteristic PDZ domain. PDZ domains are typically characterized by a defined globular structure, along with a peptide-binding site located in a groove between the αB and βB structural elements and a highly conserved carboxylate-binding loop. In contrast to other reported PDZ domains, the solution structure previously reported for IL-16 reveals a tryptophan residue obscuring the recognition groove. We have solved the structure of the 14.1Fab fragment in complex with IL-16, revealing that binding of the antibody requires a conformational change in the IL-16 PDZ domain. This involves the rotation of the αB-helix, accompanied movement of the peptide groove obscuring tryptophan residue, and consequent opening up of the binding site for interaction. Our study reveals a surprising mechanism of action for the antibody and identifies new opportunities for the development of IL-16-targeted therapeutics, including small molecules that mimic the interaction of the antibody.


  • Organizational Affiliation: 
    • From the Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, United Kingdom, gh126@le.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 59.63 kDa 
  • Atom Count: 4,339 
  • Modeled Residue Count: 525 
  • Deposited Residue Count: 544 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-IL-16 antibody 14.1 Fab domain Kappa Chain218Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-IL-16 antibody 14.1 Fab domain Heavy Chain224Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Pro-interleukin-16102Homo sapiensMutation(s): 0 
Gene Names: IL16
UniProt & NIH Common Fund Data Resources
Find proteins for Q14005 (Homo sapiens)
Explore Q14005 
Go to UniProtKB:  Q14005
PHAROS:  Q14005
GTEx:  ENSG00000172349 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14005
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
N [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.205 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.69α = 90
b = 65.95β = 90
c = 196.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-08-17
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary