9CYM: LAG3

Structure of LAG3 bound to the MHC class II molecule I-A(b). Determined by X-ray diffraction at 3.84 Å resolution. Released 21 Aug 2024.

Method: X-ray diffraction
Resolution: 3.84 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 4,778
Mol. weight: 72.94 kDa
Ligands: NAG
Released: 21 Aug 2024

Explore 9CYM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CYM contains 16 α-helices and 48 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	6
β-strand	37-42	6	6
β-strand	46-53	8	6
β-strand	56-61	6	6
β-strand	68-70	3	6
α-helix	74-77	4
α-helix	83-104	22
β-strand	112	1	7
β-strand	115-120	6	8
β-strand	130-139	10	8
β-strand	140	1	7
β-strand	144-150	7	9
β-strand	153-154	2	9
β-strand	159-161	3	8
β-strand	165-166	2	8
β-strand	172-180	9	8
β-strand	188-194	7	9
β-strand	201-205	5	9

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	34-44	11	6
β-strand	51-59	9	6
β-strand	63-68	6	6
β-strand	74-75	2	6
α-helix	79-81	3
α-helix	82-89	8
α-helix	92-101	10
α-helix	102-107	6
α-helix	108-109	2
α-helix	110-114	5
α-helix	115-117	3
β-strand	126-131	6	1
β-strand	142-150	9	1
β-strand	156-161	6	10
β-strand	164-166	3	10
β-strand	170-172	3	1
β-strand	176-177	2	1
β-strand	183-190	8	1
β-strand	199-204	6	10
β-strand	213-216	4	10

Chain L: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	1
α-helix	39-40	2
β-strand	41-42	2	2
α-helix	53-57	5
β-strand	60-66	7	1
β-strand	95-100	6	1
β-strand	106-108	3	1
α-helix	122-125	4
β-strand	130-131	2	2
α-helix	137-139	3
β-strand	141-148	8	1
β-strand	153-154	2	1
β-strand	157-163	7	1
β-strand	166-169	4	3
β-strand	175	1	4
β-strand	182-186	5	3
α-helix	192-193	2
β-strand	196-200	5	5
β-strand	205-207	3	5
β-strand	214-215	2	3
β-strand	219-221	3	3
α-helix	227-229	3
β-strand	231-237	7	5
β-strand	245-251	7	5
β-strand	253	1	4

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	92-94	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Secreted lymphocyte activation gene 3 protein	L	protein	233	Mus musculus	Q61790 (AlphaFold model)
H-2 class II histocompatibility antigen, A-B alpha chain	A	protein	195	Mus musculus	P14434 (AlphaFold model)
Class-II-associated invariant chain peptide	P	protein	16	Homo sapiens	P04233 (AlphaFold model)
H-2 class II histocompatibility antigen, A beta chain	B	protein	191	Mus musculus	P14483 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>9CYM_1 Secreted lymphocyte activation gene 3 protein (chains L)
SGPGKELPVVWAQEGAPVHLPCSLKSPNLDPNFLRRGGVIWQHQPDSGQPTPIPALDLHQ
GMPSPRQPAPGRYTVLSVAPGGLRSGRQPLHPHVQLEERGLQRGDFSLWLRPALRTDAGE
YHATVRLPNRALSCSLRLRVGQASMIASPSGVLKLSDWVLLNCSFSRPDRPVSVHWFQGQ
NRVPVYNSPRHFLAETFLLLPQVSPLDSGTWGCVLTYRDGFNVSITYNLKVLG

Sequence of entity 2 (A), FASTA

>9CYM_2 H-2 class II histocompatibility antigen, A-B alpha chain (chains A)
EDDIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDP
QGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPV
INITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLK
HWEPEIPAPMSELTE

Sequence of entity 3 (P), FASTA

>9CYM_3 Class-II-associated invariant chain peptide (chains P)
GPVSKMRMATPLLMQA

Sequence of entity 4 (B), FASTA

>9CYM_4 H-2 class II histocompatibility antigen, A beta chain (chains B)
GDSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDSDVGEHRAVTELGRPDAEY
WNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVISLSRTEALNHHNTLVCSV
TDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPS
LKSPITVEWRA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural basis for mouse LAG3 interactions with the MHC class II molecule I-A b. Ming, Q., Antfolk, D., Price, D.A. et al. Nat Commun (2024) 15:7513-7513. DOI 10.1038/s41467-024-51930-5 · PubMed

Other PDB entries of the same protein (UniProt Q61790 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TZE 2.12 Å, Structure of murine LAG3 domains 1-2
8DGG 3.78 Å, Structure of glycosylated LAG-3 homodimer
9CYL 4.66 Å, Structure of LAG3 loop1 deletion bound to the MHC class II molecule I-A(b)

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