2G9H: Staphylococcal Enterotoxin I

Crystal Structure of Staphylococcal Enterotoxin I (SEI) in Complex with a Human MHC class II Molecule. Determined by X-ray diffraction at 2.0 Å resolution. Released 11 Jul 2006.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 4
Atoms: 5,364
Mol. weight: 70.57 kDa
Ligands: ZN, DIO
Released: 11 Jul 2006

Explore 2G9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2G9H contains 22 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	57-76	20
α-helix	80-84	5
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
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, 17 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	46-49	4	1
α-helix	52-54	3
α-helix	55-61	7
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-103	6	7
β-strand	109	1	8
β-strand	112	1	8
β-strand	113-122	10	7
β-strand	123	1	6
β-strand	128-133	6	9
β-strand	136-138	3	9
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-163	9	7
β-strand	170-176	7	9
β-strand	184-189	6	9

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	2
α-helix	310-313	4
α-helix	315-317	3

Chain D: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	11-15	5
α-helix	17-18	2
β-strand	19-25	7	10
β-strand	26	1	11
β-strand	34-38	5	11
β-strand	43-47	5	11
α-helix	51-54	4
β-strand	61-66	6	10
β-strand	68	1	11
β-strand	76-79	4	11
β-strand	82-84	3	10
β-strand	88-94	7	12
α-helix	95-96	2
β-strand	97-101	5	13
β-strand	104-108	5	13
β-strand	114-117	4	12
β-strand	119-121	3	14
α-helix	122-137	16
α-helix	149-151	3
β-strand	163-170	8	13
β-strand	176-179	4	13
α-helix	188-191	4
α-helix	192-195	4
β-strand	200-202	3	14
β-strand	206-213	8	13

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, DRB1-1 beta chain	B	protein	190	Homo sapiens	P01911 (AlphaFold model)
Hemagglutinin	C	protein	13		P04664
extracellular enterotoxin type I	D	protein	218	Staphylococcus aureus	Q52T95 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2G9H_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DA

Sequence of entity 2 (B), FASTA

>2G9H_2 HLA class II histocompatibility antigen, DRB1-1 beta chain (chains B)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C), FASTA

>2G9H_3 Hemagglutinin (chains C)
PKYVKQNTLKLAT

Sequence of entity 4 (D), FASTA

>2G9H_4 extracellular enterotoxin type I (chains D)
QGDIGVGNLRNFYTKHDYIDLKGLIDKNLPSANQLEFSTGINDLISESNNWDEISKFKGK
KLDIFGIDYNGPCKSKYMYGGATLSGQYLNSARKIPINLWVNGKHKTISTDKISTNKKLV
TAQEIDVKLRRYLQEEYNIYGHNSTGKGKEYGYKSKFYSGFNKGKVLFHLNDEKSFSYDL
FYTGDGVPVSFLKIYEDNKIIESEKFHLDVEISYVDSN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
DIO	1,4-diethylene dioxide	C4 H8 O2	2

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

Primary citation

Crystal structure of staphylococcal enterotoxin I (SEI) in complex with a human major histocompatibility complex class II molecule. Fernandez, M.M., Guan, R., Swaminathan, C.P. et al. J Biol Chem (2006) 281:25356-25364. DOI 10.1074/jbc.M603969200 · 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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