5CUI

Crystal structure of Human Defensin-5 R28A mutant.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.403 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Human Enteric alpha-Defensin 5 Promotes Shigella Infection by Enhancing Bacterial Adhesion and Invasion.

Xu, D.Liao, C.Zhang, B.Tolbert, W.D.He, W.Dai, Z.Zhang, W.Yuan, W.Pazgier, M.Liu, J.Yu, J.Sansonetti, P.J.Bevins, C.L.Shao, Y.Lu, W.

(2018) Immunity --: --

  • DOI: 10.1016/j.immuni.2018.04.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Shigella is a Gram-negative bacterium that causes bacillary dysentery worldwide. It invades the intestinal epithelium to elicit intense inflammation and tissue damage, yet the underlying mechanisms of its host selectivity and low infectious inoculum ...

    Shigella is a Gram-negative bacterium that causes bacillary dysentery worldwide. It invades the intestinal epithelium to elicit intense inflammation and tissue damage, yet the underlying mechanisms of its host selectivity and low infectious inoculum remain perplexing. Here, we report that Shigella co-opts human α-defensin 5 (HD5), a host defense peptide important for intestinal homeostasis and innate immunity, to enhance its adhesion to and invasion of mucosal tissues. HD5 promoted Shigella infection in vitro in a structure-dependent manner. Shigella, commonly devoid of an effective host-adhesion apparatus, preferentially targeted HD5 to augment its ability to colonize the intestinal epithelium through interactions with multiple bacterial membrane proteins. HD5 exacerbated infectivity and Shigella-induced pathology in a culture of human colorectal tissues and three animal models. Our findings illuminate how Shigella exploits innate immunity by turning HD5 into a virulence factor for infection, unveiling a mechanism of action for this highly proficient human pathogen.


    Organizational Affiliation

    Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China; Center for Translational Medicine, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China; Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Defensin-5
A, B, C, D, E, F
32Homo sapiensMutation(s): 1 
Gene Names: DEFA5 (DEF5)
Find proteins for Q01523 (Homo sapiens)
Go to Gene View: DEFA5
Go to UniProtKB:  Q01523
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PG0
Query on PG0

Download SDF File 
Download CCD File 
A, D, E, F
2-(2-METHOXYETHOXY)ETHANOL
PEG 6000
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
C, D, E
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.403 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 59.940α = 90.00
b = 103.745β = 90.00
c = 103.985γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2018-06-13
    Type: Data collection, Database references, Derived calculations