1SEB: HLA class II histocompatibility antigen

Complex of the human MHC class II glycoprotein HLA-DR1 and the bacterial superantigen seb. Determined by X-ray diffraction at 2.7 Å resolution. Released 20 Jun 1996.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 8
Atoms: 9,396
Mol. weight: 144.65 kDa
Released: 20 Jun 1996

Explore 1SEB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SEB contains 38 α-helices and 94 β-strands across 8 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.

Chains A and E: 5 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	80-82	3
β-strand	85	1	3
α-helix	86-87	2
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	136-137	2
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	161-166	6	5
β-strand	174-178	5	5

Chains B and F: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-31	9	1
β-strand	36-41	6	1
β-strand	47-49	3	1
α-helix	55-61	7
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	6
β-strand	98-103	6	7
β-strand	113-122	10	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-137	2	8
β-strand	144	1	7
β-strand	148-149	2	7
β-strand	155-163	9	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chains C and G: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2
α-helix	3-5	3
α-helix	7-12	6

Chains D and H: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	14-16	3
α-helix	22-28	7
β-strand	33-38	6	9
β-strand	40-42	3	10
β-strand	48-51	4	10
β-strand	64-67	4	10
α-helix	71-78	8
β-strand	82-86	5	9
β-strand	89	1	10
β-strand	112-114	3	10
β-strand	117-119	3	9
β-strand	130	1	11
β-strand	150	1	11
β-strand	155-156	2	12
α-helix	157-172	16
β-strand	185-190	6	13
β-strand	195-199	5	13
α-helix	210-214	5
α-helix	215-217	3
β-strand	222-223	2	12
β-strand	229-234	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen	A, E	protein	181	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen	B, F	protein	192	Homo sapiens	P01911 (AlphaFold model)
Endogenous peptide model, poly-ala	C, G	protein	13	Homo sapiens
Enterotoxin type B	D, H	protein	234	Staphylococcus aureus	P01552 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>1SEB_1 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN (chains A, E)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
D

Sequence of entity 2 (B, F), FASTA

>1SEB_2 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN (chains B, F)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRARS

Sequence of entity 3 (C, G), FASTA

>1SEB_3 ENDOGENOUS PEPTIDE MODEL, POLY-ALA (chains C, G)
XXXXXXXXXXXXX

Sequence of entity 4 (D, H), FASTA

>1SEB_4 ENTEROTOXIN TYPE B (chains D, H)
SQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNY
DNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEH
NGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSP
YETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLT

Primary citation

Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen. Jardetzky, T.S., Brown, J.H., Gorga, J.C. et al. Nature (1994) 368:711-718. DOI 10.1038/368711a0 · 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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