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: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.4 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

  • DOI: 10.1074/jbc.270.13.7077
  • Primary Citation of Related Structures:  
    1NAP

  • 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 and platelet factor 4, binds to the interleukin-8 type II receptor and induces a rise in cytosolic calcium, chemotaxis of neutrophils, and exocytosis ...

    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 U S A 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEUTROPHIL ACTIVATING PEPTIDE-2 ABCD70Homo sapiensMutation(s): 0 
Gene Names: PPBPCTAP3CXCL7SCYB7TGB1THBGB1
Find proteins for P02775 (Homo sapiens)
Explore P02775 
Go to UniProtKB:  P02775
NIH Common Fund Data Resources
PHAROS:  P02775
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.77α = 98.37
b = 43.81β = 120.28
c = 44.65γ = 92.78
Software Package:
Software NamePurpose
GPRLSArefinement
X-PLORrefinement
X-PLORmodel building
FRODOmodel building
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-12-19
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description