Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22901.53 
• Atom Count: 1647 
• Residue Count: 206 
• Unique protein chains: 1

4IM6

LRR domain from human NLRP1

• DOI: 10.2210/pdb4IM6/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-01-02 Released: 2014-01-08 
• Deposition Author(s): Hahne, G., Reubold, T.F., Eschenburg, S.

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Experimental Data Snapshot

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

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

• PubMed: 25064844 
• 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 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.

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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: [e-mail].,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
Molecule	Chains	Sequence Length	Organism	Details
NACHT, LRR and PYD domains-containing protein 1	A	206	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

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 = 84.690	α = 90.00
b = 84.690	β = 90.00
c = 130.470	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
XSCALE	data scaling
XDS	data reduction
XDS	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-02 
• Released Date: 2014-01-08 
• Deposition Author(s): Hahne, G., Reubold, T.F., Eschenburg, S.

Revision History 

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