Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58828.92 
• Atom Count: 4134 
• Residue Count: 503 
• Unique protein chains: 4

1P4L

Crystal structure of NK receptor Ly49C mutant with its MHC class I ligand H-2Kb

• DOI: 10.2210/pdb1P4L/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2003-04-23 Released: 2003-11-11 
• Deposition Author(s): Dam, J., Guan, R., Natarajan, K., Dimasi, N., Mariuzza, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.295 
• R-Value Work: 0.269 

Literature

Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2K(b).

Dam, J., Guan, R., Natarajan, K., Dimasi, N., Chlewicki, L.K., Kranz, D.M., Schuck, P., Margulies, D.H., Mariuzza, R.A.

(2003) Nat.Immunol. 4: 1213-1222

• PubMed: 14595439 
• DOI: 10.1038/ni1006
• Primary Citation of Related Structures:  
  1P1Z


• PubMed Abstract: 
  

The Ly49 family of natural killer (NK) receptors regulates NK cell function by sensing major histocompatibility complex (MHC) class I. Ly49 receptors show complex patterns of MHC class I cross-reactivity and, in certain cases, peptide selectivity. To investigate whether specificity differences result from topological differences in MHC class I engagement, we determined the structure of the peptide-selective receptor Ly49C in complex with H-2K(b). The Ly49C homodimer binds two MHC class I molecules in symmetrical way, a mode distinct from that of Ly49A, which binds MHC class I asymmetrically. Ly49C does not directly contact the MHC-bound peptide. In addition, MHC crosslinking by Ly49C was demonstrated in solution. We propose a dynamic model for Ly49-MHC class I interactions involving conformational changes in the receptor, whereby variations in Ly49 dimerization mediate different MHC-binding modes.

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, W.M. Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MHC CLASS I H-2KB HEAVY CHAIN	A	274	Mus musculus	Mutation(s): 0  Gene Names: H2-K1 (H2-K)
Find proteins for P01901 (Mus musculus) Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Go to UniProtKB:  P01887

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Ovalbumin peptide	P	8	Gallus gallus	Mutation(s): 0  Gene Names: SERPINB14
Find proteins for P01012 (Gallus gallus) Go to UniProtKB:  P01012

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
LY49-C	D	122	Mus musculus	Mutation(s): 3  Gene Names: Klra3 (Ly-49c, Ly49C)
Find proteins for Q64329 (Mus musculus) Go to UniProtKB:  Q64329

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.295 
• R-Value Work: 0.269 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 152.010	α = 90.00
b = 152.010	β = 90.00
c = 64.660	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-23 
• Released Date: 2003-11-11 
• Deposition Author(s): Dam, J., Guan, R., Natarajan, K., Dimasi, N., Mariuzza, R.A.

Revision History 

• Version 1.0: 2003-11-11
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance