Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 130699.88 
• Atom Count: 7879 
• Residue Count: 1120 
• Unique protein chains: 2

6O3O

Structure of human DNAM-1 (CD226) bound to nectin-like protein-5 (necl-5)

• DOI: 10.2210/pdb6O3O/pdb

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


• Deposited: 2019-02-27 Released: 2019-07-10 
• Deposition Author(s): Deuss, F.A., Watson, G.M., Rossjohn, J., Berry, R.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia); Australian Research Council (ARC) 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.231 
• R-Value Work: 0.208 

Literature

Structural basis for the recognition of nectin-like protein-5 by the human-activating immune receptor, DNAM-1.

Deuss, F.A., Watson, G.M., Goodall, K.J., Leece, I., Chatterjee, S., Fu, Z., Thaysen-Andersen, M., Andrews, D.M., Rossjohn, J., Berry, R.

(2019) J.Biol.Chem. 294: 12534-12546

• PubMed: 31253644 
• DOI: 10.1074/jbc.RA119.009261


• PubMed Abstract: 
  

Nectin and nectin-like (NECL) adhesion molecules are broadly overexpressed in a wide range of cancers. By binding to these adhesion molecules, the immunoreceptors DNAX accessory molecule-1 (DNAM-1), CD96 molecule (CD96), and T cell immunoreceptor with Ig and ITIM domains (TIGIT) play a crucial role in regulating the anticancer activities of immune effector cells. However, within this axis, it remains unclear how DNAM-1 recognizes its cognate ligands. Here, we determined the structure of human DNAM-1 in complex with nectin-like protein-5 (NECL-5) at 2.8 Å resolution. Unexpectedly, we found that the two extracellular domains (D1-D2) of DNAM-1 adopt an unconventional "collapsed" arrangement that is markedly distinct from those in other immunoglobulin-based immunoreceptors. The DNAM-1:NECL-5 interaction was underpinned by conserved lock-and-key motifs located within their respective D1 domains, but also included a distinct interface derived from DNAM-1 D2. Mutation of the signature DNAM-1 "key" motif within the D1 domain attenuated NECL-5 binding and natural killer cell-mediated cytotoxicity. Altogether, our results have implications for understanding the binding mode of an immune receptor family that is emerging as a viable candidate for cancer immunotherapy.

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Organizational Affiliation: 

Monash University, Australia.,Biochemistry & Molecular Biology, Monash University, Australia.,Monash University.,Macquarie University, Australia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CD226 antigen	A, B	243	Homo sapiens	Mutation(s): 0  Gene Names: CD226 (DNAM1)
Find proteins for Q15762 (Homo sapiens) Go to Gene View: CD226 Go to UniProtKB:  Q15762

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Poliovirus receptor	C, D	317	Homo sapiens	Mutation(s): 0  Gene Names: PVR (PVS)
Find proteins for P15151 (Homo sapiens) Go to Gene View: PVR Go to UniProtKB:  P15151

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MAN	D	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	C, D	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
BMA	C, D	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, B, C, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.231 
• R-Value Work: 0.208 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 129.337	α = 90.00
b = 182.269	β = 90.00
c = 146.594	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-02-27 
• Released Date: 2019-07-10 
• Deposition Author(s): Deuss, F.A., Watson, G.M., Rossjohn, J., Berry, R.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1109901
Australian Research Council (ARC)	Australia	FL160100049

Revision History 

• Version 1.0: 2019-07-10
  Type: Initial release
• Version 1.1: 2019-08-28
  Type: Data collection, Database references
• Version 1.2: 2020-01-01
  Type: Author supporting evidence, Data collection