1QE6

INTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (L5C/H33C)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Receptor-binding conformation of the "ELR" motif of IL-8: X-ray structure of the L5C/H33C variant at 2.35 A resolution.

Gerber, N.Lowman, H.Artis, D.R.Eigenbrot, C.

(2000) Proteins 38: 361-367

  • Primary Citation of Related Structures:  
    1QE6

  • PubMed Abstract: 
  • The "ELR" (Glu-Leu-Arg) tripeptide sequence near the N-terminus of interleukin-8 (IL-8) contributes a large part of the receptor binding free energy. Prior X-ray and nuclear magnetic resonance (NMR) structures of IL-8 have shown this region of the mo ...

    The "ELR" (Glu-Leu-Arg) tripeptide sequence near the N-terminus of interleukin-8 (IL-8) contributes a large part of the receptor binding free energy. Prior X-ray and nuclear magnetic resonance (NMR) structures of IL-8 have shown this region of the molecule to be highly mobile. We reasoned that a hydrophobic interaction between the leucine and the neighboring beta-turn might exist in the receptor binding conformation of the N-terminus. To test this hypothesis, we mutated two residues to cysteine and connected the N-terminus to the beta-turn. The mutant retains receptor binding affinity reasonably close to wild type and allows the characterization of a high-affinity conformation that may be useful in the design of small IL-8 mimics. The L5C/H33C mutant is refined to R-values of R = 20.6% and Rfree = 27.7% at 2.35 A resolution. Other receptor binding determinants reside in the "N-loop" found after "ELR" and preceding the first beta-strand. All available structures of IL-8 have been found with one of two distinct N-loop conformations. One of these is relevant for receptor binding, based on NMR results with receptor peptides. The other conformation obscures the receptor-peptide binding surface and may have an undetermined but necessarily different function.


    Related Citations: 
    • Crystal structure of IL-8:Symbiosis of NMR and crystallography
      Baldwin, E.T., Weber, I.T., Charles, R.St., Xuan, J.-C.
      (1991) Proc Natl Acad Sci U S A 88: 502
    • Structural change and receptor binding in a chemokine mutant with a re- arranged disulfide: X-ray structure of E38C/C50A IL-8 at 2 A resolution.
      Eigenbrot, C., Lowman, H.B., Chee, L., Artis, D.R.
      (1997) Proteins 27: 556

    Organizational Affiliation

    Department of Protein Engineering Genentech, Inc., South San Francisco, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INTERLEUKIN-8 VARIANTABCD72Homo sapiensMutation(s): 0 
Gene Names: CXCL8IL8
Find proteins for P10145 (Homo sapiens)
Explore P10145 
Go to UniProtKB:  P10145
NIH Common Fund Data Resources
PHAROS  P10145
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.54α = 90
b = 71.77β = 90.46
c = 57.86γ = 90
Software Package:
Software NamePurpose
MCCDATAdata collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
MCCDATAdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Advisory, Experimental preparation