1HKF | pdb_00001hkf

The three dimensional structure of NK cell receptor Nkp44, a triggering partner in natural cytotoxicity

• PDB DOI: https://doi.org/10.2210/pdb1HKF/pdb

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


• Deposited: 2003-03-10 Released: 2003-06-11 
• Deposition Author(s): Ponassi, M., Cantoni, C., Biassoni, R., Conte, R., Spallarossa, A., Moretta, A., Moretta, L., Bolognesi, M., Bordo, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.245 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

The Three-Dimensional Structure of the Human Nk Cell Receptor Nkp44, a Triggering Partner in Natural Cytotoxicity

Cantoni, C., Ponassi, M., Biassoni, R., Conte, R., Spallarossa, A., Moretta, A., Moretta, L., Bolognesi, M., Bordo, D.

(2003) Structure 11: 725

• PubMed: 12791260 
• DOI: https://doi.org/10.1016/s0969-2126(03)00095-9
• Primary Citation of Related Structures:  
  1HKF


• PubMed Abstract: 
  

  Natural killer (NK) cells direct cytotoxicity against tumor or virally infected cells. NK cell activation depends on a fine balance between inhibitory and activating receptors. NKp44 is a cytotoxicity activating receptor composed of one Ig-like extracellular domain, a transmembrane segment, and a cytoplasmic domain. The 2.2 A crystal structure shows that the NKp44 Ig domain forms a saddle-shaped dimer, where a charged surface groove protrudes from the core structure in each subunit. NKp44 Ig domain disulfide bridge topology defines a new Ig structural subfamily. The data presented are a first step toward understanding the molecular basis for ligand recognition by natural cytotoxicity receptors, whose key role in the immune system is established, but whose cellular ligands are still elusive.

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Organizational Affiliation: 
• Dipartimento di Medicina Sperimentale, Università di Genova, Via L.B. Alberti 1, 16132 Genova, Italy.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.96 kDa 
• Atom Count: 981 
• Modeled Residue Count: 108 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NK CELL ACTIVATING RECEPTOR	A	122	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O95944 (Homo sapiens) Explore O95944  Go to UniProtKB:  O95944
GTEx:  ENSG00000096264

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.245 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.437	α = 90
b = 60.437	β = 90
c = 197.253	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-11 
Deposition Author(s): Ponassi, M., Cantoni, C., Biassoni, R., Conte, R., Spallarossa, A., Moretta, A., Moretta, L., Bolognesi, M., Bordo, D.

Revision History  

• Version 1.0: 2003-06-11
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Other, Structure summary