1DFN

CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHANISMS OF MEMBRANE PERMEABILIZATION

• PDB DOI:  https://doi.org/10.2210/pdb1DFN/pdb

• Classification: DEFENSIN
• Organism(s): Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1991-01-18 Released: 1992-07-15 
• Deposition Author(s): Hill, C.P., Yee, J., Selsted, M.E., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 0.190 

Literature

Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization.

Hill, C.P., Yee, J., Selsted, M.E., Eisenberg, D.

(1991) Science 251: 1481-1485

• PubMed: 2006422 
• DOI: https://doi.org/10.1126/science.2006422
• Primary Citation of Related Structures:  
  1DFN


• PubMed Abstract: 
  

Defensins (molecular weight 3500 to 4000) act in the mammalian immune response by permeabilizing the plasma membranes of a broad spectrum of target organisms, including bacteria, fungi, and enveloped viruses. The high-resolution crystal structure of defensin HNP-3 (1.9 angstrom resolution, R factor 0.19) reveals a dimeric beta sheet that has an architecture very different from other lytic peptides. The dimeric assembly suggests mechanisms by which defensins might bind to and permeabilize the lipid bilayer.

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Related Citations: 

• Primary Structures of Three Human Neutrophil Defensins
  Selsted, M.E., Harwig, S.S.L., Ganz, T., Schilling, J.W., Lehrer, R.I.
  (1985) J Clin Invest 76: 1436

• Defensins. Natural Peptide Antibiotics of Human Neutrophils
  Ganz, T., Selsted, M.E., Szklarek, D., Harwig, S.S.L., Daher, K., Bainton, D.F., Lehrer, R.I.
  (1985) J Clin Invest 76: 1427

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Organizational Affiliation: 

Eisenberg, Molecular Biology Institute, Los Angeles, CA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 6.99 kDa 
• Atom Count: 514 
• Modelled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEFENSIN HNP-3	A, B	30	Homo sapiens	Mutation(s): 0  Gene Names: DEFA3, DEF3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59666 (Homo sapiens) Explore P59666  Go to UniProtKB:  P59666
PHAROS:  P59666

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.8	α = 90
b = 45	β = 90
c = 40.3	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-07-15 
Deposition Author(s): Hill, C.P., Yee, J., Selsted, M.E., Eisenberg, D.

Revision History  

• Version 1.0: 1992-07-15
  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: 2017-11-29
  Changes: Derived calculations, Other