Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78144.43 
• Atom Count: 5338 
• Residue Count: 683 
• Unique protein chains: 4

5B39

KIR3DL1*015 in complex with HLA-B*57:01

• DOI: 10.2210/pdb5B39/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Enterobacteria phage L1


• Deposited: 2016-02-12 Released: 2016-03-30 
• Deposition Author(s): Vivian, J.P., Rossjohn, J.
• Funding Organization(s): National Health and Medical Research Council (Australia) 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.229 
• R-Value Work: 0.178 

Literature

Killer cell immunoglobulin-like receptor 3DL1 polymorphism defines distinct hierarchies of HLA class I recognition

Saunders, P.M., Pymm, P., Pietra, G., Hughes, V.A., Hitchen, C., O'Connor, G.M., Loiacono, F., Widjaja, J., Price, D.A., Falco, M., Mingari, M.C., Moretta, L., McVicar, D.W., Rossjohn, J., Brooks, A.G., Vivian, J.P.

(2016) J.Exp.Med. 213: 791-807

• PubMed: 27045007 
• DOI: 10.1084/jem.20152023
• Primary Citation of Related Structures:  
  5B38


• PubMed Abstract: 
  

Natural killer (NK) cells play a key role in immunity, but how HLA class I (HLA-I) and killer cell immunoglobulin-like receptor 3DL1 (KIR3DL1) polymorphism impacts disease outcome remains unclear. KIR3DL1 (*001/*005/*015) tetramers were screened for reactivity against a panel of HLA-I molecules. This revealed different and distinct hierarchies of specificity for each KIR3DL1 allotype, with KIR3DL1*005 recognizing the widest array of HLA-I ligands. These differences were further reflected in functional studies using NK clones expressing these specific KIR3DL1 allotypes. Unexpectedly, the Ile/Thr80 dimorphism in the Bw4-motif did not categorically define strong/weak KIR3DL1 recognition. Although the KIR3DL1*001, *005, and *015 polymorphisms are remote from the KIR3DL1-HLA-I interface, the structures of these three KIR3DL1-HLA-I complexes showed that the broader HLA-I specificity of KIR3DL1*005 correlated with an altered KIR3DL1*005 interdomain positioning and increased mobility within its ligand-binding site. Collectively, we provide a generic framework for understanding the impact of KIR3DL1 polymorphism on the recognition of HLA-I allomorphs.

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Organizational Affiliation: 

Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class I histocompatibility antigen, B-57 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B (HLAB)
Find proteins for P18465 (Homo sapiens) Go to Gene View: HLA-B Go to UniProtKB:  P18465

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
peptide from Ig kappa chain C region	C	9	Homo sapiens	Mutation(s): 0  Gene Names: IGKC
Find proteins for P01834 (Homo sapiens) Go to UniProtKB:  P01834

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Killer cell immunoglobulin-like receptor 3DL1	G	299	Homo sapiens	Mutation(s): 0  Gene Names: KIR3DL1 (CD158E, NKAT3, NKB1)
Find proteins for P43629 (Homo sapiens) Go to Gene View: KIR3DL1 Go to UniProtKB:  P43629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	G	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.229 
• R-Value Work: 0.178 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 51.568	α = 95.56
b = 61.118	β = 98.50
c = 65.089	γ = 108.65

Software Package:

Software Name	Purpose
PHASER	phasing
SCALA	data scaling
PHENIX	refinement
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-02-12 
• Released Date: 2016-03-30 
• Deposition Author(s): Vivian, J.P., Rossjohn, J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (Australia)	Australia	1099814

Revision History 

• Version 1.0: 2016-03-30
  Type: Initial release
• Version 1.1: 2016-04-20
  Type: Database references
• Version 1.2: 2016-05-18
  Type: Database references
• Version 1.3: 2017-10-18
  Type: Author supporting evidence, Data collection, Database references, Derived calculations