1HQR: Superantigen

Crystal structure of a superantigen bound to the high-affinity, zinc-dependent site on MHC class II. Determined by X-ray diffraction at 3.2 Å resolution. Released 3 Jan 2001.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Streptococcus pyogenes
Chains: 4
Atoms: 4,539
Mol. weight: 69.32 kDa
Ligands: ZN
Released: 3 Jan 2001

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

Secondary structure: helices and β-sheets

1HQR contains 19 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: 2 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	48-50	3
β-strand	53	1	2
α-helix	56-76	21
β-strand	88	1	3
β-strand	91-93	3	3
β-strand	103-112	10	3
β-strand	118-124	7	4
β-strand	126-127	2	4
β-strand	134	1	3
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174	1	4
β-strand	177-178	2	4

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	207-218	12	1
β-strand	223-232	10	1
β-strand	235-241	7	1
β-strand	247-249	3	1
α-helix	252-254	3
α-helix	255-261	7
α-helix	265-272	8
α-helix	274	1
α-helix	275-280	6
α-helix	281-286	6
α-helix	287-289	3
β-strand	295	1	5
β-strand	299-302	4	6
β-strand	313-322	10	6
β-strand	323	1	5
β-strand	328-333	6	7
β-strand	336-337	2	7
β-strand	342-344	3	6
β-strand	348-349	2	6
β-strand	355-363	9	6
β-strand	370-377	8	7
β-strand	380-389	10	7

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	408	1	2

Chain D: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	506-517	12
β-strand	522	1	8
β-strand	527-529	3	9
β-strand	538-540	3	9
α-helix	541-543	3
β-strand	551-554	4	9
α-helix	557-560	4
β-strand	568-571	4	9
β-strand	573	1	8
β-strand	575	1	9
β-strand	585-587	3	9
β-strand	590-592	3	9
α-helix	593-594	2
β-strand	600-601	2	10
α-helix	602-603	2
β-strand	604-609	6	11
β-strand	611	1	11
α-helix	612-613	2
β-strand	615	1	11
β-strand	621-622	2	10
β-strand	626-628	3	12
α-helix	629-644	16
β-strand	655-662	8	11
β-strand	669	1	11
α-helix	681-684	4
α-helix	687-690	4
β-strand	693-695	3	12
α-helix	696-698	3
β-strand	699-707	9	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA-dr alpha chain	A	protein	181	Homo sapiens	P01903 (AlphaFold model)
HLA-dr beta chain	B	protein	190	Homo sapiens	Q30154 (AlphaFold model)
Myelin basic protein	C	protein	13	Homo sapiens	P02686 (AlphaFold model)
Streptococcal pyrogenic exotoxin C	D	protein	208	Streptococcus pyogenes	Q8NKX2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1HQR_1 HLA-DR ALPHA CHAIN (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
D

Sequence of entity 2 (B), FASTA

>1HQR_2 HLA-DR BETA CHAIN (chains B)
GDTRPRFLQQDKYECHFFNGTERVRFLHRDIYNQEEDLRFDSDVGEYRAVTELGRPDAEY
WNSQKDFLEDRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPARTQTLQHHNLLVCSVN
GFYPGSIEVRWFRNSQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C), FASTA

>1HQR_3 MYELIN BASIC PROTEIN (chains C)
VHFFKNIVTPRTP

Sequence of entity 4 (D), FASTA

>1HQR_4 STREPTOCOCCAL PYROGENIC EXOTOXIN C (chains D)
DSKKDISNVKSDLLYAYTITPYDYKDCRVNFSTTHTLNIDTQKYRGKDYYISSEMSYEAS
QKFKRDDHVDVFGLFYILNSHTGEYIYGGITPAQNNKVNHKLLGNLFISGESQQNLNNKI
ILEKDIVTFQEIDFKIRKYLMDNYKIYDATSPYVSGRIEIGTKDGKHEQIDLFDSPNEGT
RSDIFAKYKDNRIINMKNFSHFDIYLEK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Crystal structure of a superantigen bound to the high-affinity, zinc-dependent site on MHC class II. Li, Y., Li, H., Dimasi, N. et al. Immunity (2001) 14:93-104. DOI 10.1016/S1074-7613(01)00092-9 · 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

Browse structure collections

About this viewer

MolViewer shows 1HQR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.