2NZ7 | pdb_00002nz7

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

• PDB DOI: https://doi.org/10.2210/pdb2NZ7/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-22 Released: 2007-12-04 
• Deposition Author(s): Thiagarajan, S., Robbins, S.L., Dubas, R.L., Park, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.266 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

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

• PubMed: 18186648 
• DOI: https://doi.org/10.1021/bi7016602
• Primary Citation Related Structures: 
  2NZ7


• 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 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.

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Organizational Affiliation: 
• Basic Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.73 kDa 
• Atom Count: 1,622 
• Modeled Residue Count: 191 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase recruitment domain-containing protein 4	A, B	98	Homo sapiens	Mutation(s): 0  Gene Names: CARD4, NOD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y239 (Homo sapiens) Explore Q9Y239  Go to UniProtKB:  Q9Y239
PHAROS:  Q9Y239 GTEx:  ENSG00000106100

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.266 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.091	α = 90
b = 79.091	β = 90
c = 80.863	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Thiagarajan, S., Robbins, S.L., Dubas, R.L., Park, Y.C.

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary