4JQW

Crystal Structure of a Complex of NOD1 CARD and Ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb4JQW/pdb

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


• Deposited: 2013-03-20 Released: 2014-03-26 
• Deposition Author(s): Ver Heul, A.M., Gakhar, L., Piper, R.C., Ramaswamy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.270 
• R-Value Work: 0.226 
• R-Value Observed: 0.230 

Starting Models: experimental

Literature

Crystal structure of a complex of NOD1 CARD and ubiquitin

Ver Heul, A.M., Gakhar, L., Piper, R.C., Ramaswamy, S.

(2014) PLoS One 9: e104017-e104017

• PubMed: 25127239 
• DOI: https://doi.org/10.1371/journal.pone.0104017
• Primary Citation of Related Structures:  
  4JQW


• PubMed Abstract: 
  

  The Caspase Recruitment Domain (CARD) from the innate immune receptor NOD1 was crystallized with Ubiquitin (Ub). NOD1 CARD was present as a helix-swapped homodimer similar to other structures of NOD1 CARD, and Ub monomers formed a homodimer similar in conformation to Lys48-linked di-Ub. The interaction between NOD1 CARD and Ub in the crystal was mediated by novel binding sites on each molecule. Comparisons of these sites to previously identified interaction surfaces on both molecules were made along with discussion of their potential functional significance.

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Organizational Affiliation: 

Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa, United States of America; Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.71 kDa 
• Atom Count: 1,338 
• Modelled Residue Count: 165 
• Deposited Residue Count: 178 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotide-binding oligomerization domain-containing protein 1	A	102	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	B [auth C]	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS	A	L-PEPTIDE LINKING	C5 H12 As N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.270 
• R-Value Work: 0.226 
• R-Value Observed: 0.230 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.688	α = 90
b = 61.688	β = 90
c = 86.873	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Ver Heul, A.M., Gakhar, L., Piper, R.C., Ramaswamy, S.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary