2NNA: MHC class II molecule HLA-DQ8

Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 4 Sept 2007.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,382
Mol. weight: 46.84 kDa
Released: 4 Sept 2007

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

Secondary structure: helices and β-sheets

2NNA contains 15 α-helices and 30 β-strands across 3 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, 14 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	46-51	6
β-strand	53	1	2
α-helix	56-76	21
α-helix	81-87	7
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	132-134	3	3
α-helix	137	1
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-178	5	4

Chain B: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	0-2	3
α-helix	4-5	2
β-strand	8-18	11	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-87	7
α-helix	90-92	3
β-strand	95	1	5
α-helix	96-97	2
β-strand	98-102	5	6
β-strand	115-122	8	6
β-strand	123	1	5
β-strand	128-133	6	7
β-strand	136-137	2	7
β-strand	142-144	3	6
α-helix	145-147	3
β-strand	148-149	2	6
β-strand	155-161	7	6
β-strand	171-176	6	7
β-strand	184-188	5	7

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2
α-helix	3-4	2
α-helix	8-12	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II antigen	A	protein	184	Homo sapiens	P01909 (AlphaFold model)
MHC class II antigen	B	protein	207	Homo sapiens	P01920 (AlphaFold model)
gluten peptide	C	protein	18		P18573 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2NNA_1 MHC class II antigen (chains A)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPE

Sequence of entity 2 (B), FASTA

>2NNA_2 MHC class II antigen (chains B)
GGGGSIEGRGSGGGSRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVG
VYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSR
TEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTP
QRGDVYTCHVEHPSLQNPIIVEWRAQS

Sequence of entity 3 (C), FASTA

>2NNA_3 gluten peptide (chains C)
QQYPSGEGSFQPSQENPQ

Primary citation

A structural and immunological basis for the role of human leukocyte antigen DQ8 in celiac disease. Henderson, K.N., Tye-Din, J.A., Reid, H.H. et al. Immunity (2007) 27:23-34. DOI 10.1016/j.immuni.2007.05.015 · 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
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
1S9V 2.22 Å, Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide
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

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