4MTH

Crystal structure of mature human RegIIIalpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Antibacterial membrane attack by a pore-forming intestinal C-type lectin.

Mukherjee, S.Zheng, H.Derebe, M.G.Callenberg, K.M.Partch, C.L.Rollins, D.Propheter, D.C.Rizo, J.Grabe, M.Jiang, Q.X.Hooper, L.V.

(2013) Nature 505: 103-107

  • DOI: 10.1038/nature12729

  • PubMed Abstract: 
  • Human body-surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins. C-type lectins of the RegIII family are bactericidal proteins that limit direct contact between bac ...

    Human body-surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins. C-type lectins of the RegIII family are bactericidal proteins that limit direct contact between bacteria and the intestinal epithelium and thus promote tolerance to the intestinal microbiota. RegIII lectins recognize their bacterial targets by binding peptidoglycan carbohydrate, but the mechanism by which they kill bacteria is unknown. Here we elucidate the mechanistic basis for RegIII bactericidal activity. We show that human RegIIIα (also known as HIP/PAP) binds membrane phospholipids and kills bacteria by forming a hexameric membrane-permeabilizing oligomeric pore. We derive a three-dimensional model of the RegIIIα pore by docking the RegIIIα crystal structure into a cryo-electron microscopic map of the pore complex, and show that the model accords with experimentally determined properties of the pore. Lipopolysaccharide inhibits RegIIIα pore-forming activity, explaining why RegIIIα is bactericidal for Gram-positive but not Gram-negative bacteria. Our findings identify C-type lectins as mediators of membrane attack in the mucosal immune system, and provide detailed insight into an antibacterial mechanism that promotes mutualism with the resident microbiota.


    Organizational Affiliation

    Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regenerating islet-derived protein 3-alpha 15 kDa form
A
139Homo sapiensMutation(s): 0 
Gene Names: REG3A (HIP, PAP, PAP1)
Find proteins for Q06141 (Homo sapiens)
Go to Gene View: REG3A
Go to UniProtKB:  Q06141
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.762α = 90.00
b = 49.528β = 90.00
c = 92.152γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-09-19 
  • Released Date: 2013-11-27 
  • Deposition Author(s): Derebe, M.G.

Revision History 

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description