4IM6

LRR domain from human NLRP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the leucine-rich repeat domain of the NOD-like receptor NLRP1: implications for binding of muramyl dipeptide.

Reubold, T.F.Hahne, G.Wohlgemuth, S.Eschenburg, S.

(2014) Febs Lett. 588: 3327-3332

  • DOI: 10.1016/j.febslet.2014.07.017

  • PubMed Abstract: 
  • The NOD-like receptor NLRP1 (NLR family, pyrin domain containing 1) senses the presence of the bacterial cell wall component l-muramyl dipeptide (MDP) inside the cell. We determined the crystal structure of the LRR domain of human NLRP1 in the absenc ...

    The NOD-like receptor NLRP1 (NLR family, pyrin domain containing 1) senses the presence of the bacterial cell wall component l-muramyl dipeptide (MDP) inside the cell. We determined the crystal structure of the LRR domain of human NLRP1 in the absence of MDP to a resolution of 1.65Å. The fold of the structure can be assigned to the ribonuclease inhibitor-like class of LRR proteins. We compared our structure with X-ray models of the LRR domains of NLRX1 and NLRC4 and a homology model of the LRR domain of NOD2. We conclude that the MDP binding site of NLRP1 is not located in the LRR domain.


    Organizational Affiliation

    Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany. Electronic address: Eschenburg.Susanne@MH-Hannover.de.,Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NACHT, LRR and PYD domains-containing protein 1
A
206Homo sapiensMutation(s): 0 
Gene Names: NLRP1 (CARD7, DEFCAP, KIAA0926, NAC, NALP1)
Find proteins for Q9C000 (Homo sapiens)
Go to Gene View: NLRP1
Go to UniProtKB:  Q9C000
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.134 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 84.690α = 90.00
b = 84.690β = 90.00
c = 130.470γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
XDSdata reduction
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2019-08-07
    Type: Data collection, Database references, Derived calculations