2NDK

20 lowest energy ensemble of dermcidin (DCD1L) NMR structure


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the bacterial membrane insertion of dermcidin peptide, DCD-1L.

Nguyen, V.S.Tan, K.W.Ramesh, K.Chew, F.T.Mok, Y.K.

(2017) Sci Rep 7: 13923-13923

  • DOI: 10.1038/s41598-017-13600-z

  • PubMed Abstract: 
  • Human dermcidin (DCD) is an antimicrobial peptide secreted constitutively by sweat glands. The anionic derivative, DCD-1L, comprises of the N-terminal 47 residues of DCD and one additional leucine residue. A previous NMR structure of DCD-1L in 50% TF ...

    Human dermcidin (DCD) is an antimicrobial peptide secreted constitutively by sweat glands. The anionic derivative, DCD-1L, comprises of the N-terminal 47 residues of DCD and one additional leucine residue. A previous NMR structure of DCD-1L in 50% TFE showed a partial helical conformation, and its crystal structure in the presence of Zn2+ outlined a hexameric linear α-helical bundle. Three different models to describe membrane insertion were proposed but no conclusion was drawn. In the current study, the NMR structure of DCD-1L in SDS micelles showed an "L-shaped" molecule with three fully formed α-helices connected by flexible turns. Formation of these helices in DCD-1L in the presence of POPG vesicles suggests that the acidic C-terminal region of DCD-1L can suppress the binding of DCD-1L to POPG vesicles at basic but not acidic pH. Mutation of charged residues on the N-terminal and C-terminal regions of DCD-1L cause differences in POPG binding, suggesting distinct functional roles for these two regions. Charged residues from these two regions are also found to differentially affect Zn2+ coordination and aggregation of DCD-1L in the absence or presence of SDS, as monitored by 1D NMR. Our data agrees with one of the three models proposed.


    Organizational Affiliation

    Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dermcidin
A
48Homo sapiensMutation(s): 0 
Gene Names: DCD (AIDD, DSEP)
EC: 3.4.-.-
Find proteins for P81605 (Homo sapiens)
Go to Gene View: DCD
Go to UniProtKB:  P81605
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-29 
  • Released Date: 2017-07-05 
  • Deposition Author(s): Tan, K., Mok, Y.

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references