1HXY: Staphylococcal enterotoxin H

Crystal structure of staphylococcal enterotoxin H in complex with human MHC class II. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 Jun 2001.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 4
Atoms: 4,828
Mol. weight: 69.5 kDa
Ligands: ZN
Released: 27 Jun 2001

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

Secondary structure: helices and β-sheets

1HXY contains 21 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: 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	126-127	2	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: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
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	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-102	5	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	142-144	3	7
β-strand	148-149	2	7
β-strand	155-163	9	7
β-strand	170-176	7	8
α-helix	183	1
β-strand	184-189	6	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	2
α-helix	311-317	7

Chain D: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-8	3
α-helix	11-22	12
β-strand	25-30	6	9
β-strand	35	1	10
β-strand	40-43	4	10
α-helix	48-50	3
β-strand	52-56	5	10
α-helix	60-66	7
β-strand	71-75	5	9
β-strand	77-78	2	10
β-strand	90-94	5	10
β-strand	97-99	3	9
β-strand	103-116	14	11
β-strand	119-120	2	11
β-strand	124-130	7	11
β-strand	132-134	3	12
α-helix	135-150	16
β-strand	161-168	8	11
β-strand	173-177	5	11
α-helix	186-189	4
α-helix	190-193	4
β-strand	198-200	3	12
α-helix	201-203	3
β-strand	204-212	9	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, dr alpha chain	A	protein	182	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, dr-1 beta chain	B	protein	190	Homo sapiens	P01911 (AlphaFold model)
Hemagglutinin	C	protein	13		Q03909
Enterotoxin H	D	protein	213	Staphylococcus aureus	P0A0M0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1HXY_1 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DA

Sequence of entity 2 (B), FASTA

>1HXY_2 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1 BETA CHAIN (chains B)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C), FASTA

>1HXY_3 HEMAGGLUTININ (chains C)
PKYVKQNTLKLAT

Sequence of entity 4 (D), FASTA

>1HXY_4 ENTEROTOXIN H (chains D)
EDLHDKSELTDLALANAYGQYNHPFIKENIKSDEISGEKDLIFRNQGDSGNDLRVKFATA
DLAQKFKNKNVDIYGASFYYKCEKISENISECLYGGTTLNSEKLAQERVIGANVWVDGIQ
KETELIRTNKKNVTLQELDIKIRKILSDKYKIYYKDSEISKGLIEFDMKTPRDYSFDIYD
LKGENDYEIDKIYEDNKTLKSDDISHIDVNLYT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Crystal Structure of a Superantigen Bound to MHC Class II Displays Zinc and Peptide Dependence. Petersson, K., Hakansson, M., Nilsson, H. et al. EMBO J (2001) 20:3306-3312. DOI 10.1093/emboj/20.13.3306 · 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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