1KWI | pdb_00001kwi

Crystal Structure Analysis of the Cathelicidin Motif of Protegrins

• PDB DOI: https://doi.org/10.2210/pdb1KWI/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Sus scrofa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-01-29 Released: 2002-10-09 
• Deposition Author(s): Sanchez, J.F., Hoh, F., Strub, M.P., Aumelas, A., Dumas, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.291 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Structure of the cathelicidin motif of protegrin-3 precursor: structural insights into the activation mechanism of an antimicrobial protein.

Sanchez, J.F., Hoh, F., Strub, M.P., Aumelas, A., Dumas, C.

(2002) Structure 10: 1363-1370

• PubMed: 12377122 
• DOI: https://doi.org/10.1016/s0969-2126(02)00859-6
• Primary Citation Related Structures: 
  1KWI, 1LXE


• PubMed Abstract: 
  

  Cathelicidins are a family of antimicrobial proteins isolated from leucocytes and epithelia cells that contribute to the innate host defense mechanisms in mammalians. Located in the C-terminal part of the holoprotein, the cathelicidin-derived antimicrobial peptide is liberated by a specific protease cleavage. Here, we report the X-ray structure of the cathelicidin motif of protegrin-3 solved by MAD phasing using the selenocysteine-labeled protein. Its overall structure represents a fold homologous to the cystatin family and adopts two native states, a monomer, and a domain-swapped dimer. This crystal structure is the first example of a structural characterization of the highly conserved cathelicidin motif and thus provides insights into the possible mechanism of activation of the antimicrobial protegrin peptide.

---

Organizational Affiliation: 
• Centre de Biochimie Structurale, UMR CNRS 5048, UMR 554 INSERM, Université Montpellier I, 15 Avenue Charles Flahault, 34060 Montpellier Cedex, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.32 kDa 
• Atom Count: 741 
• Modeled Residue Count: 85 
• Deposited Residue Count: 101 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protegrin-3 Precursor	A	101	Sus scrofa	Mutation(s): 0  Gene Names: pg3
UniProt
Find proteins for P32196 (Sus scrofa) Explore P32196  Go to UniProtKB:  P32196

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.291 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.36	α = 90
b = 51.36	β = 90
c = 133.677	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
CNS	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-09 
Deposition Author(s): Sanchez, J.F., Hoh, F., Strub, M.P., Aumelas, A., Dumas, C.

Revision History  

• Version 1.0: 2002-10-09
  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: 2024-11-20
  Changes: Data collection, Database references, Structure summary