2NZ7

Crystal Structure Analysis of Caspase-recruitment Domain (CARD) of Nod1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Monomer/dimer transition of the caspase-recruitment domain of human Nod1

Srimathi, T.Robbins, S.L.Dubas, R.L.Hasegawa, M.Inohara, N.Park, Y.C.

(2008) Biochemistry 47: 1319-1325

  • DOI: 10.1021/bi7016602

  • PubMed Abstract: 
  • Nod1 is an essential cytoplasmic sensor for bacterial peptidoglycans in the innate immune system. The caspase-recruitment domain of Nod1 (Nod1_CARD) is indispensable for recruiting a downstream kinase, receptor-interacting protein 2 (RIP2), that acti ...

    Nod1 is an essential cytoplasmic sensor for bacterial peptidoglycans in the innate immune system. The caspase-recruitment domain of Nod1 (Nod1_CARD) is indispensable for recruiting a downstream kinase, receptor-interacting protein 2 (RIP2), that activates nuclear factor-kappaB (NF-kappaB). The crystal structure of human Nod1_CARD at 1.9 A resolution reveals a novel homodimeric conformation. Our structural and biochemical analysis shows that the homodimerization of Nod1_CARD is achieved by swapping the H6 helices at the carboxy termini and stabilized by forming an interchain disulfide bond between the Cys39 residues of the two monomers in solution and in the crystal. In addition, we present experimental evidence for a pH-sensitive conformational change of Nod1_CARD. Our results suggest that the pH-sensitive monomer/dimer transition is a unique molecular property of Nod1_CARD.


    Organizational Affiliation

    Basic Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase recruitment domain-containing protein 4
A, B
98Homo sapiensGene Names: NOD1 (CARD4)
Find proteins for Q9Y239 (Homo sapiens)
Go to Gene View: NOD1
Go to UniProtKB:  Q9Y239
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.091α = 90.00
b = 79.091β = 90.00
c = 80.863γ = 120.00
Software Package:
Software NamePurpose
RESOLVEphasing
REFMACrefinement
SCALAdata scaling
HKL-2000data scaling
DENZOdata reduction
SOLVEphasing
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance