1TVX

NEUTROPHIL ACTIVATING PEPTIDE-2 VARIANT FORM M6L WITH FIVE ADDITIONAL AMINO TERMINAL RESIDUES (DSDLY)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The amino-terminal residues in the crystal structure of connective tissue activating peptide-III (des10) block the ELR chemotactic sequence.

Malkowski, M.G.Lazar, J.B.Johnson, P.H.Edwards, B.F.

(1997) J.Mol.Biol. 266: 367-380

  • DOI: 10.1006/jmbi.1996.0796

  • PubMed Abstract: 
  • alpha-Chemokines comprise a family of cytokines that are chemotactic for neutrophils and have a structure similar to platelet factor 4 (PF4), in which the first two cysteine residues are separated by one residue (Cys-X-Cys). The two alpha-chemokines, ...

    alpha-Chemokines comprise a family of cytokines that are chemotactic for neutrophils and have a structure similar to platelet factor 4 (PF4), in which the first two cysteine residues are separated by one residue (Cys-X-Cys). The two alpha-chemokines, connective tissue activating peptide-III (CTAP-III) and neutrophil activating peptide-2 (NAP-2), are carboxyl-terminal fragments of platelet basic protein (PBP) that are generated by monocyte-derived proteases. NAP-2 strongly stimulates neutrophils that are present during inflammation whereas its precursors, PBP and CTAP-III, are inactive, although they also possess the highly conserved, amino-terminal sequence, Glu-Leu-Arg (ELR), that is critical for receptor binding. To resolve this conundrum, we have determined the crystal structure of recombinant Asp-CTAP, which has ten fewer amino-terminal residues than CTAP-III but five more than NAP-2. The space group is P2(1)with unit cell dimensions a = 43.8 A, b = 76.8 A, c = 43.8 A, and beta =97.0 degrees, and a tetramer in the asymmetric unit. The molecular replacement method, with the NAP-2 tetramer as a starting model, was used to determine the initial phase information. The final R-factor is 0.196 (Rfree = 0.251) for 2sigma data from 7.0 to 1.75 A resolution. This high-resolution model of Asp-CTAP is the longest defined structure of an alpha-chemokine to date. The electron density map shows an over-all structure for Asp-CTAP that is very similar to that of NAP-2, but with the additional five amino-terminal residues folding back through a type-II turn, thereby stabilizing the oligomeric "inactive" state, and masking the critical ELR receptor binding region that is exposed in the structure of NAP-2.


    Related Citations: 
    • The Crystal Structure of Recombinant Human Neutrophil-Activating Peptide-2 (M6L) at 1.9-A Resolution
      Malkowski, M.G.,Wu, J.Y.,Lazar, J.B.,Johnson, P.H.,Edwards, B.F.
      (1995) J.Biol.Chem. 270: 7077
    • The Three-Dimensional Structure of Bovine Platelet Factor 4 at 3.0-A Resolution
      Charles, R.St.,Walz, D.A.,Edwards, B.F.
      (1989) J.Biol.Chem. 264: 2092
    • Crystal Structure of Interleukin 8: Symbiosis of NMR and Crystallography
      Baldwin, E.T.,Weber, I.T.,Charles, R.St.,Xuan, J.C.,Appella, E.,Yamada, M.,Matsushima, K.,Edwards, B.F.,Clore, G.M.,Gronenborn, A.M.,al., et
      (1991) Proc.Natl.Acad.Sci.USA 88: 502


    Organizational Affiliation

    Department of Biochemistry, Wayne State University, Canfield, Detroit, MI 48201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUTROPHIL ACTIVATING PEPTIDE 2 VARIANT
A, B, C, D
75Homo sapiensMutation(s): 0 
Gene Names: PPBP (CTAP3, CXCL7, SCYB7, TGB1, THBGB1)
Find proteins for P02775 (Homo sapiens)
Go to Gene View: PPBP
Go to UniProtKB:  P02775
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.810α = 90.00
b = 76.760β = 96.95
c = 43.780γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata collection
X-PLORphasing
XENGENdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance