9CYL

Structure of LAG3 loop1 deletion bound to the MHC class II molecule I-A(b)

• PDB DOI: https://doi.org/10.2210/pdb9CYL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-08-02 Released: 2024-08-21 
• Deposition Author(s): Ming, Q., Tran, T.H., Antfolk, D., Luca, V.C.
• Funding Organization(s): Other government, Rita Allen Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.66 Å
• R-Value Free: 0.326 
• R-Value Work: 0.268 
• R-Value Observed: 0.271 

Starting Model: experimental

Literature

Structural basis for LAG3 interactions with MHC class II

Ming, Q., Tran, T.H., Antfolk, D., Luca, V.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 70.55 kDa 
• Atom Count: 4,699 
• Modelled Residue Count: 590 
• Deposited Residue Count: 612 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-B alpha chain	A	195	Mus musculus	Mutation(s): 0  Gene Names: H2-Aa
UniProt
Find proteins for P14434 (Mus musculus) Explore P14434  Go to UniProtKB:  P14434
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A beta chain	B	192	Mus musculus	Mutation(s): 0  Gene Names: H2-Ab1, H2-iabeta
UniProt
Find proteins for P14483 (Mus musculus) Explore P14483  Go to UniProtKB:  P14483
Glycosylation
Glycosylation Sites: 1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Class-II-associated invariant chain peptide	C [auth P]	15	Homo sapiens	Mutation(s): 0  Gene Names: CD74, DHLAG
UniProt & NIH Common Fund Data Resources
Find proteins for P04233 (Homo sapiens) Explore P04233  Go to UniProtKB:  P04233
PHAROS:  P04233 GTEx:  ENSG00000019582

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Secreted lymphocyte activation gene 3 protein	D [auth L]	210	Mus musculus	Mutation(s): 0  Gene Names: Lag3
UniProt
Find proteins for Q61790 (Mus musculus) Explore Q61790  Go to UniProtKB:  Q61790
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q61790-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth B], G [auth L], H [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.66 Å
• R-Value Free: 0.326 
• R-Value Work: 0.268 
• R-Value Observed: 0.271 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.994	α = 90
b = 184.994	β = 90
c = 122.672	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Ming, Q., Tran, T.H., Antfolk, D., Luca, V.C.

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Funding Organization	Location	Grant Number
Other government	United States	Florida Department of Health Bankhead-Coley 22B07
Rita Allen Foundation	United States	--

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release