8DGG: Glycosylated LAG-3 homodimer

Structure of glycosylated LAG-3 homodimer. Determined by X-ray diffraction at 3.78 Å resolution. Released 17 Aug 2022.

Method: X-ray diffraction
Resolution: 3.78 Å
Organism: Mus musculus
Chains: 2
Atoms: 5,049
Mol. weight: 95.15 kDa
Ligands: FUC, NAG
Released: 17 Aug 2022

Explore 8DGG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DGG contains 8 α-helices and 65 β-strands across 2 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: 3 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	1
β-strand	40-42	3	2
β-strand	60-65	6	1
β-strand	96-100	5	1
β-strand	106-107	2	1
β-strand	116-118	3	2
α-helix	129	1
β-strand	130-132	3	2
β-strand	141-148	8	1
β-strand	153-163	11	1
β-strand	165-170	6	3
β-strand	175	1	4
β-strand	181-187	7	3
β-strand	197-200	4	5
β-strand	205-207	3	5
β-strand	214-215	2	3
β-strand	219-222	4	3
β-strand	232-236	5	5
β-strand	246-250	5	5
β-strand	253	1	4
β-strand	263-267	5	6
β-strand	273-274	2	7
α-helix	278-279	2
β-strand	290-291	2	8
β-strand	302-303	2	8
β-strand	312-313	2	7
α-helix	319-321	3
β-strand	324	1	6
β-strand	327-330	4	8
β-strand	335-338	4	8
β-strand	341-349	9	6
β-strand	360-366	7	6
β-strand	373-378	6	9
β-strand	386-387	2	9
β-strand	390-392	3	6
β-strand	403-409	7	9
β-strand	412-417	6	9

Chain B: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	10
β-strand	36	1	11
β-strand	40-42	3	12
α-helix	55-58	4
β-strand	61-65	5	10
β-strand	96-101	6	10
β-strand	105-107	3	10
α-helix	111	1
β-strand	116-118	3	12
α-helix	123-125	3
β-strand	130-132	3	12
β-strand	135	1	11
α-helix	137-139	3
β-strand	141-147	7	10
β-strand	156-163	8	10
β-strand	166-167	2	13
β-strand	170	1	14
β-strand	175	1	15
β-strand	181-184	4	14
β-strand	185-186	2	13
β-strand	197-200	4	16
β-strand	205-206	2	16
β-strand	214-216	3	14
β-strand	219-222	4	14
α-helix	227-230	4
β-strand	232-236	5	16
β-strand	246-250	5	16
β-strand	253	1	15
β-strand	272-274	3	17
β-strand	277	1	18
β-strand	309	1	18
β-strand	312-314	3	17
β-strand	324	1	19
β-strand	329-330	2	20
β-strand	335-336	2	20
β-strand	341	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lymphocyte activation gene 3 protein	A, B	protein	426	Mus musculus	Q61790 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8DGG_1 Lymphocyte activation gene 3 protein (chains A, B)
SGPGKELPVVWAQEGAPVHLPCSLKSPNLDPNFLRRGGVIWQHQPDSGQPTPIPALDLHQ
GMPSPRQPAPGRYTVLSVAPGGLRSGRQPLHPHVQLEERGLQRGDFSLWLRPALRTDAGE
YHATVRLPNRALSCSLRLRVGQASMIASPSGVLKLSDWVLLNCSFSRPDRPVSVHWFQGQ
NRVPVYNSPRHFLAETFLLLPQVSPLDSGTWGCVLTYRDGFNVSITYNLKVLGLEPVAPL
TVYAAEGSRVELPCHLPPGVGTPSLLIAKWTPPGGGPELPVAGKSGNFTLHLEAVGLAQA
GTYTCSIHLQGQQLNATVTLAVITVTPKSFGLPGSRGKLLCEVTPASGKERFVWRPLNNL
SRSCPGPVLEIQEARLLAERWQCQLYEGQRLLGATVYAAESSSGAHSARRISGDLKGGHL
HHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
FUC	alpha-L-fucopyranose	C6 H12 O5	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function. Silberstein, J.L., Du, J., Chan, K.W. et al. Proc Natl Acad Sci U S A (2024) 121:e2310866121-e2310866121. DOI 10.1073/pnas.2310866121 · 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
9CYM 3.84 Å, Structure of LAG3 bound to the MHC class II molecule I-A(b)
9CYL 4.66 Å, Structure of LAG3 loop1 deletion bound to the MHC class II molecule I-A(b)

Browse structure collections

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