4IM6 | pdb_00004im6

LRR domain from human NLRP1

• PDB DOI: https://doi.org/10.2210/pdb4IM6/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.febslet.2014.07.017
• Primary Citation Related Structures: 
  4IM6


• 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.
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].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.9 kDa 
• Atom Count: 1,860 
• Modeled Residue Count: 198 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NACHT, LRR and PYD domains-containing protein 1	A	206	Homo sapiens	Mutation(s): 0  Gene Names: CARD7, DEFCAP, KIAA0926, NAC, NALP1, NLRP1 EC: 3.6.4 (UniProt), 3.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C000 (Homo sapiens) Explore Q9C000  Go to UniProtKB:  Q9C000
PHAROS:  Q9C000 GTEx:  ENSG00000091592

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL 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 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.69	α = 90
b = 84.69	β = 90
c = 130.47	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary