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 1.2 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
  • Primary Citation of Related Structures:  
    2NDK

  • 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% TFE showed a partial helical conformation, and its crystal structure in the presence of Zn 2+ outlined a hexameric linear α-helical bundle ...

    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 Zn 2+ 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 Zn 2+ 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. dbsmokh@nus.edu.sg.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DermcidinA48Homo sapiensMutation(s): 0 
Gene Names: DCDAIDDDSEP
EC: 3.4
Find proteins for P81605 (Homo sapiens)
Explore P81605 
Go to UniProtKB:  P81605
NIH Common Fund Data Resources
PHAROS:  P81605
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2NDK Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Experimental preparation, Structure summary