9CYM | pdb_00009cym

Structure of LAG3 bound to the MHC class II molecule I-A(b)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 
    0.307 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for mouse LAG3 interactions with the MHC class II molecule I-A b.

Ming, Q.Antfolk, D.Price, D.A.Manturova, A.Medina, E.Singh, S.Mason, C.Tran, T.H.Smalley, K.S.M.Leung, D.W.Luca, V.C.

(2024) Nat Commun 15: 7513-7513

  • DOI: https://doi.org/10.1038/s41467-024-51930-5
  • Primary Citation of Related Structures:  
    9CYL, 9CYM

  • PubMed Abstract: 

    The immune checkpoint protein, Lymphocyte activation gene-3 (LAG3), binds Major Histocompatibility Complex Class II (MHC-II) and suppresses T cell activation. Despite the recent FDA approval of a LAG3 inhibitor for the treatment of melanoma, how LAG3 engages MHC-II on the cell surface remains poorly understood. Here, we determine the 3.84 Å-resolution structure of mouse LAG3 bound to the MHC-II molecule I-A b , revealing that domain 1 (D1) of LAG3 binds a conserved, membrane-proximal region of MHC-II spanning both the α2 and β2 subdomains. LAG3 dimerization restricts the intermolecular spacing of MHC-II molecules, which may attenuate T cell activation by enforcing suboptimal signaling geometry. The LAG3-MHC-II interface overlaps with the MHC-II-binding site of the T cell coreceptor CD4, implicating disruption of CD4-MHC-II interactions as a mechanism for LAG3 immunosuppressive function. Lastly, antibody epitope analysis indicates that multiple LAG3 inhibitors do not recognize the MHC-II-binding interface of LAG3, suggesting a role for functionally distinct mechanisms of LAG3 antagonism in therapeutic development.


  • Organizational Affiliation

    Moffitt Cancer Center and Research Institute, Department of Immunology, Tampa, FL, 33612, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Secreted lymphocyte activation gene 3 proteinA [auth L]233Mus musculusMutation(s): 0 
Gene Names: Lag3
UniProt
Find proteins for Q61790 (Mus musculus)
Explore Q61790 
Go to UniProtKB:  Q61790
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61790
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q61790-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-B alpha chainB [auth A]195Mus musculusMutation(s): 0 
Gene Names: H2-Aa
UniProt
Find proteins for P14434 (Mus musculus)
Explore P14434 
Go to UniProtKB:  P14434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14434
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Class-II-associated invariant chain peptideC [auth P]16Homo sapiensMutation(s): 0 
Gene Names: CD74DHLAG
UniProt & NIH Common Fund Data Resources
Find proteins for P04233 (Homo sapiens)
Explore P04233 
Go to UniProtKB:  P04233
PHAROS:  P04233
GTEx:  ENSG00000019582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04233
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A beta chainD [auth B]191Mus musculusMutation(s): 0 
Gene Names: H2-Ab1H2-iabeta
UniProt
Find proteins for P14483 (Mus musculus)
Explore P14483 
Go to UniProtKB:  P14483
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14483
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free:  0.307 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.652α = 90
b = 187.652β = 90
c = 124.057γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesBankhead-Coley grant from the Florida Department of Health, Grant # 22B07
Rita Allen FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary