1NAP

THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING PEPTIDE-2 (M6L) AT 1.9-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 7077-7087


  • PubMed Abstract: 
  • Neutrophil-activating peptide-2 (NAP-2) is a 70-residue carboxyl-terminal fragment of platelet basic protein, which is found in the alpha-granules of human platelets. NAP-2, which belongs to the CXC family of chemokines that includes interleukin-8 an ...

    Neutrophil-activating peptide-2 (NAP-2) is a 70-residue carboxyl-terminal fragment of platelet basic protein, which is found in the alpha-granules of human platelets. NAP-2, which belongs to the CXC family of chemokines that includes interleukin-8 and platelet factor 4, binds to the interleukin-8 type II receptor and induces a rise in cytosolic calcium, chemotaxis of neutrophils, and exocytosis. Crystals of recombinant NAP-2 in which the single methionine at position 6 was replaced by leucine to facilitate expression belong to space group P1 (unit cell parameters a = 40.8, b = 43.8, and c = 44.7 A and alpha = 98.4 degrees, beta = 120.3 degrees, and gamma = 92.8 degrees), with 4 molecules of NAP-2 (Mr = 7600) in the asymmetric unit. The molecular replacement solution calculated with bovine platelet factor 4 as the starting model was refined using rigid body refinement, manual fitting in solvent-leveled electron density maps, simulated annealing, and restrained least squares to an R-factor of 0.188 for 2 sigma data between 7.0- and 1.9-A resolution. The final refined crystal structure includes 265 solvent molecules. The overall tertiary structure, which is similar to that of platelet factor 4 and interleukin-8, includes an extended amino-terminal loop, three strands of antiparallel beta-sheet arranged in a Greek key fold, and one alpha-helix at the carboxyl terminus. The Glu-Leu-Arg sequence that is critical for receptor binding is fully defined by electron density and exhibits multiple conformations.


    Related Citations: 
    • The Three Dimensional Structure of Bovine Platelet Factor 4 at 3.0 Angstroms Resolution
      Charles, R.St.,Walz, D.A.,Edwards, B.F.P.
      (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.P.,Clore, G.M.,Gronenborn, A.M.,Wlodawer, A.
      (1991) Proc.Natl.Acad.Sci.USA 88: 502
    • Three Dimensional Structure of Interleukin 8 in Solution
      Clore, G.M.,Appella, E.,Yamada, M.,Matsushima, K.,Gronenborn, A.M.
      (1990) Biochemistry 29: 1689


    Organizational Affiliation

    Department of Biochemistry, Wayne State University, Detroit, Michigan 48201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUTROPHIL ACTIVATING PEPTIDE-2
A, B, C, D
70Homo sapiensGene 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: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.770α = 98.37
b = 43.810β = 120.28
c = 44.650γ = 92.78
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
FRODOmodel building
X-PLORmodel building
GPRLSArefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-19
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance