9BF9: Human LAG-3-HLA-DR1 complex

Human LAG-3-HLA-DR1 complex. Determined by X-ray diffraction at 3.4 Å resolution. Released 25 Dec 2024.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 4,865
Mol. weight: 94.22 kDa
Ligands: NAG
Released: 25 Dec 2024

Explore 9BF9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BF9 contains 17 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: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-50	5
β-strand	53	1	2
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	3
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-128	3	5
β-strand	133-134	2	4
α-helix	137	1
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-79	5
α-helix	80-85	6
β-strand	95	1	6
β-strand	98-104	7	7
β-strand	114-122	9	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-137	2	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-162	8	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain D: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	9
β-strand	18-20	3	10
β-strand	38-44	7	9
α-helix	74-76	3
β-strand	77-82	6	9
β-strand	90	1	7
β-strand	98-100	3	10
α-helix	102-106	5
β-strand	112-114	3	10
α-helix	119-121	3
β-strand	123-130	8	9
β-strand	135-145	11	9
β-strand	147-151	5	11
α-helix	154-156	3
β-strand	163-169	7	11
α-helix	174-175	2
β-strand	177-183	7	12
β-strand	188-191	4	12
β-strand	194	1	13
β-strand	197	1	13
β-strand	198-199	2	11
β-strand	203-206	4	11
β-strand	218-222	5	12
β-strand	228-232	5	12

Chain G: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2
α-helix	3-5	3
α-helix	10-12	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	189	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen DR beta chain	B	protein	211	Homo sapiens	D7RIG0 (AlphaFold model)
Membrane protein	G	protein	13	Severe acute respiratory syndrome coronavirus 2	P0DTC5 (AlphaFold model)
Lymphocyte activation gene 3 protein	D	protein	418	Homo sapiens	P18627 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9BF9_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DTSGDDDDK

Sequence of entity 2 (B), FASTA

>9BF9_2 HLA class II histocompatibility antigen DR beta chain (chains B)
DSGGSGSIEGRGSGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEY
RAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQ
PLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRS
GEVYTCQVEHPSVTSPLTVEWRATGGDDDDK

Sequence of entity 3 (G), FASTA

>9BF9_3 Membrane protein (chains G)
SYYKLGASQRVAG

Sequence of entity 4 (D), FASTA

>9BF9_4 Lymphocyte activation gene 3 protein (chains D)
GSLQPGAEVPVVWAQEGAPAQLPCSPTIPLQDLSLLRRAGVTWQHQPDSGPPAAAPGHPL
APGPHPAAPSSWGPRPRRYTVLSVGPGGLRSGRLPLQPRVQLDERGRQRGDFSLWLRPAR
RADAGEYRAAVHLRDRALSCRLRLRLGQASMTASPPGSLRASDWVILNCSFSRPDRPASV
HWFRNRGQGRVPVRESPHHHLAESFLFLPQVSPMDSGPWGCILTYRDGFNVSIMYNLTVL
GLEPPTPLTVYAGAGSRVGLPCRLPAGVGTRSFLTAKWTPPGGGPDLLVTGDNGDFTLRL
EDVSQAQAGTYTCHIHLQEQQLNATVTLAIITVTPKSFGSPGSLGKLLCEVTPVSGQERF
VWSSLDTPSQRSFSGPWLEAQEAQLLSQPWQCQLYQGERLLGAAVYFTETGGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (SO4, PEG) are not listed.

Primary citation

Crystal structure of the human LAG-3-HLA-DR1-peptide complex. Petersen, J., Llerena, C., Golzarroshan, B. et al. Sci Immunol (2024) 9:eads5122-eads5122. DOI 10.1126/sciimmunol.ads5122 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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