9CYL: LAG3 loop1 deletion

Structure of LAG3 loop1 deletion bound to the MHC class II molecule I-A(b). Determined by X-ray diffraction at 4.66 Å resolution. Released 21 Aug 2024.

Method: X-ray diffraction
Resolution: 4.66 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 4,699
Mol. weight: 70.55 kDa
Ligands: NAG
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

9CYL contains 16 α-helices and 51 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: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	31-42	12	1
β-strand	46-52	7	1
β-strand	57-61	5	1
β-strand	68-70	3	1
α-helix	73-76	4
α-helix	83-103	21
α-helix	106-110	5
β-strand	112	1	2
α-helix	113-114	2
β-strand	115-120	6	3
β-strand	130-139	10	3
β-strand	140	1	2
β-strand	144-150	7	4
β-strand	154	1	4
β-strand	160-161	2	3
α-helix	162-164	3
β-strand	165-166	2	3
β-strand	172-180	9	3
β-strand	188-194	7	4
β-strand	201-205	5	4

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	34-45	12	1
β-strand	50-59	10	1
β-strand	63-68	6	1
β-strand	74-76	3	1
α-helix	82-88	7
α-helix	92-101	10
α-helix	102-107	6
α-helix	108-110	3
α-helix	112-115	4
β-strand	122	1	5
β-strand	125-129	5	6
β-strand	140-149	10	6
β-strand	150	1	5
β-strand	155-160	6	7
β-strand	164-165	2	7
β-strand	169-172	4	6
β-strand	175-176	2	6
β-strand	182-190	9	6
β-strand	198-203	6	7
β-strand	211-215	5	7

Chain L: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	8
β-strand	42-43	2	9
α-helix	53-56	4
β-strand	60-63	4	6
β-strand	64-67	4	8
β-strand	98-100	3	6
β-strand	106-108	3	6
α-helix	112-113	2
α-helix	122-124	3
β-strand	129-130	2	9
β-strand	141-144	4	8
β-strand	147-148	2	6
β-strand	153-154	2	6
β-strand	157-162	6	8
β-strand	166-169	4	10
β-strand	175	1	11
β-strand	182-186	5	10
α-helix	192-193	2
β-strand	196-200	5	12
β-strand	205-207	3	12
β-strand	214-216	3	10
β-strand	219-221	3	10
α-helix	227-229	3
β-strand	231-237	7	12
β-strand	248-251	4	12
β-strand	253	1	11

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	92-95	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-B alpha chain	A	protein	195	Mus musculus	P14434 (AlphaFold model)
H-2 class II histocompatibility antigen, A beta chain	B	protein	192	Mus musculus	P14483 (AlphaFold model)
Class-II-associated invariant chain peptide	P	protein	15	Homo sapiens	P04233 (AlphaFold model)
Secreted lymphocyte activation gene 3 protein	L	protein	210	Mus musculus	Q61790 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9CYL_1 H-2 class II histocompatibility antigen, A-B alpha chain (chains A)
EDDIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDP
QGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPV
INITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLK
HWEPEIPAPMSELTE

Sequence of entity 2 (B), FASTA

>9CYL_2 H-2 class II histocompatibility antigen, A beta chain (chains B)
GGDSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDSDVGEHRAVTELGRPDAE
YWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVISLSRTEALNHHNTLVCS
VTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHP
SLKSPITVEWRA

Sequence of entity 3 (P), FASTA

>9CYL_3 Class-II-associated invariant chain peptide (chains P)
PVSKMRMATPLLMQA

Sequence of entity 4 (L), FASTA

>9CYL_4 Secreted lymphocyte activation gene 3 protein (chains L)
SGPGKELPVVWAQEGAPVHLPCSLKSPNLDPNFLRRGGVIWQHQPDSGGRYTVLSVAPGG
LRSGRQPLHPHVQLEERGLQRGDFSLWLRPALRTDAGEYHATVRLPNRALSCSLRLRVGQ
ASMIASPSGVLKLSDWVLLNCSFSRPDRPVSVHWFQGQNRVPVYNSPRHFLAETFLLLPQ
VSPLDSGTWGCVLTYRDGFNVSITYNLKVL

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 P14434 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VQ8 2.01 Å, Immune receptor complex
8RAL 2.1 Å, CL3E peptide bound to the I-Ab murine MHC class II receptor
1MUJ 2.15 Å, Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide
4P23 2.25 Å, J809.B5 TCR bound to IAb/3K
1LNU 2.5 Å, Crystal structure of class II MHC molecule iab bound to EALPHA3K peptide
3C5Z 2.55 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506
6MNG 2.66 Å, 4738 TCR bound to IAb Padi4
3RDT 2.7 Å, Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide
6MNN 2.83 Å, 6236 TCR bound to I-Ab Padi4
4P46 2.85 Å, J809.B5 Y31A TCR bound to IAb3K
6MNO 2.9 Å, 6235 TCR bound to I-Ab Padi4
9AUD 2.9 Å, Immune receptor complex

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