Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 130.50 kDa 
• Atom Count: 7982 
• Modelled Residue Count: 993 
• Deposited 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: Homo sapiens, Trichoplusia ni
• Mutation(s): No 


• 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: 2.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

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
• Primary Citation of Related Structures:  
  6O3O


• 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: 

Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD226 antigen	A, B	243	Homo sapiens	Mutation(s): 0  Gene Names: CD226, DNAM1
Find proteins for Q15762 (Homo sapiens) Explore Q15762  Go to UniProtKB:  Q15762
NIH Common Fund Data Resources
PHAROS:  Q15762 GTEx:  ENSG00000150637

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Poliovirus receptor	C, D	317	Homo sapiens	Mutation(s): 0  Gene Names: PVR, PVS
Find proteins for P15151 (Homo sapiens) Explore P15151  Go to UniProtKB:  P15151
NIH Common Fund Data Resources
PHAROS:  P15151 GTEx:  ENSG00000073008

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	4		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A],  J [auth A],  K [auth A],  L [auth A],  O [auth B],  P [auth B],  Q [auth C],  R [auth C],  S [auth C],  T [auth C],  U [auth D],  V [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	M [auth A], N [auth A], W [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.337	α = 90
b = 182.269	β = 90
c = 146.594	γ = 90

Software Package:

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

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
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary