5V52 | pdb_00005v52

Structure of TIGIT bound to nectin-2 (CD112)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.236 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.8 of the entry. See complete history

Literature

Recognition of nectin-2 by the natural killer cell receptor T cell immunoglobulin and ITIM domain (TIGIT).

Deuss, F.A.Gully, B.S.Rossjohn, J.Berry, R.

(2017) J Biological Chem 292: 11413-11422

  • DOI: https://doi.org/10.1074/jbc.M117.786483
  • Primary Citation Related Structures: 
    5V52

  • PubMed Abstract: 

    T cell immunoglobulin and ITIM domain (TIGIT) is an inhibitory receptor expressed on the surface of natural killer (NK) cells. TIGIT recognizes nectin and nectin-like adhesion molecules and thus plays a critical role in the innate immune response to malignant transformation. Although the TIGIT nectin-like protein-5 (necl-5) interaction is well understood, how TIGIT engages nectin-2, a receptor that is broadly over-expressed in breast and ovarian cancer, remains unknown. Here, we show that TIGIT bound to the immunoglobulin domain of nectin-2 that is most distal from the membrane with an affinity of 6 μm, which was moderately lower than the affinity observed for the TIGIT/necl-5 interaction (3.2 μm). The TIGIT/nectin-2 binding disrupted pre-assembled nectin-2 oligomers, suggesting that receptor-ligand and ligand-ligand associations are mutually exclusive events. Indeed, the crystal structure of TIGIT bound to the first immunoglobulin domain of nectin-2 indicated that the receptor and ligand dock using the same molecular surface and a conserved "lock and key" binding motifs previously observed to mediate nectin/nectin homotypic interactions as well as TIGIT/necl-5 recognition. Using a mutagenesis approach, we dissected the energetic basis for the TIGIT/nectin-2 interaction and revealed that an "aromatic key" of nectin-2 is critical for this interaction, whereas variations in the lock were tolerated. Moreover, we found that the C-C' loop of the ligand dictates the TIGIT binding hierarchy. Altogether, these findings broaden our understanding of nectin/nectin receptor interactions and have implications for better understanding the molecular basis for autoimmune disease and cancer.


  • Organizational Affiliation
    • From the Infection and Immunity Program, Biomedicine Discovery Institute and.

Macromolecule Content 

  • Total Structure Weight: 54.39 kDa 
  • Atom Count: 3,443 
  • Modeled Residue Count: 459 
  • Deposited Residue Count: 494 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell immunoreceptor with Ig and ITIM domains
A, B
107Homo sapiensMutation(s): 1 
Gene Names: TIGITVSIG9VSTM3
UniProt & NIH Common Fund Data Resources
Find proteins for Q495A1 (Homo sapiens)
Explore Q495A1 
Go to UniProtKB:  Q495A1
PHAROS:  Q495A1
GTEx:  ENSG00000181847 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ495A1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nectin-2
C, D
140Homo sapiensMutation(s): 0 
Gene Names: NECTIN2HVEBPRR2PVRL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92692 (Homo sapiens)
Explore Q92692 
Go to UniProtKB:  Q92692
PHAROS:  Q92692
GTEx:  ENSG00000130202 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92692
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q92692-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.236 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.5α = 90
b = 68.5β = 90
c = 253.91γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1109901

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references
  • Version 1.2: 2017-07-19
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2020-02-26
    Changes: Data collection
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.7: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.8: 2024-10-30
    Changes: Structure summary