1S9V: HLA-DQ2

Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide. Determined by X-ray diffraction at 2.22 Å resolution. Released 2 Mar 2004.

Method: X-ray diffraction
Resolution: 2.22 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,330
Mol. weight: 92.64 kDa
Released: 2 Mar 2004

Explore 1S9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1S9V contains 27 α-helices and 56 β-strands across 6 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	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
α-helix	56-76	21
α-helix	81-87	7
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-127	2	3
β-strand	132-134	3	2
α-helix	137	1
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	161-166	6	3
β-strand	174-178	5	3

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	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	55-63	9
α-helix	65-71	7
α-helix	74	1
α-helix	75-80	6
α-helix	81-87	7
α-helix	90-92	3
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-103	6	5
β-strand	114-122	9	5
β-strand	123	1	4
β-strand	128-132	5	6
β-strand	137-138	2	6
β-strand	142-144	3	5
β-strand	148-149	2	5
β-strand	155-162	8	5
β-strand	170-176	7	6
β-strand	184-189	6	6

Chains C and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8

Chain D: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	7
β-strand	19-26	8	7
β-strand	29-35	7	7
β-strand	40-43	4	7
α-helix	46-50	5
α-helix	57-76	20
α-helix	81-87	7
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	118-123	6	9
β-strand	126-127	2	9
α-helix	128	1
β-strand	132-134	3	8
α-helix	137	1
β-strand	138-139	2	8
β-strand	145-153	9	8
β-strand	161-166	6	9
β-strand	174-177	4	9

Chain E: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	7
β-strand	23-32	10	7
β-strand	35-41	7	7
β-strand	47-49	3	7
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	10
α-helix	96-97	2
β-strand	98-103	6	11
β-strand	114-122	9	11
β-strand	123	1	10
β-strand	128-133	6	12
β-strand	136-138	3	12
β-strand	142-144	3	11
α-helix	145-147	3
β-strand	148-149	2	11
β-strand	155-162	8	11
β-strand	170-176	7	12
β-strand	184-189	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ(3) alpha chain	A, D	protein	193	Homo sapiens	P01909 (AlphaFold model)
HLA class II histocompatibility antigen, DQ(1) beta chain	B, E	protein	198	Homo sapiens	P01920 (AlphaFold model)
alpha-I gliadin	C, F	protein	11

Sequence of entity 1 (A, D), FASTA

>1S9V_1 HLA class II histocompatibility antigen, DQ(3) alpha chain (chains A, D)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPEIPAPMSELTE

Sequence of entity 2 (B, E), FASTA

>1S9V_2 HLA class II histocompatibility antigen, DQ(1) beta chain (chains B, E)
RDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEY
WNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QSPITVEWRAQSESAQSK

Sequence of entity 3 (C, F), FASTA

>1S9V_3 alpha-I gliadin (chains C, F)
LQPFPQPELPY

Primary citation

Structural basis for HLA-DQ2-mediated presentation of gluten epitopes in celiac disease. Kim, C.-Y., Quarsten, H., Bergseng, E. et al. Proc Natl Acad Sci U S A (2004) 101:4175-4179. DOI 10.1073/pnas.0306885101 · PubMed

Other PDB entries of the same protein (UniProt P01909 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6U3M 1.9 Å, DQ2-P.fluor-alpha1a
5KSA 2.0 Å, Bel602-DQ8.5-glia-gamma1 complex
6MFG 2.0 Å, HLA-DQ2-glia-alpha1
2NNA 2.1 Å, Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide
8W84 2.1 Å, HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02
5KSV 2.19 Å, Crystal structure of HLA-DQ2.5-CLIP2
9EJG 2.2 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
8W86 2.24 Å, HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02
1JK8 2.4 Å, Crystal structure of a human insulin peptide-HLA-DQ8 complex
6XP6 2.4 Å, 3C11-DQ2-glia-a2 complex
9EJH 2.45 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
6MFF 2.6 Å, HLA-DQ2-glia-omega1

Browse structure collections

About this viewer

MolViewer shows 1S9V 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.