4JQW

Crystal Structure of a Complex of NOD1 CARD and Ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1371/journal.pone.0104017

  • 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 i ...

    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.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleotide-binding oligomerization domain-containing protein 1
A
102Homo sapiensMutation(s): 0 
Gene Names: NOD1 (CARD4)
Find proteins for Q9Y239 (Homo sapiens)
Go to Gene View: NOD1
Go to UniProtKB:  Q9Y239
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
C
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.688α = 90.00
b = 61.688β = 90.00
c = 86.873γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
d*TREKdata scaling
Blu-Icedata collection
PHENIXrefinement
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references