4D8P: HLA-DQA1 protein

Structural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) molecule. Determined by X-ray diffraction at 3.05 Å resolution. Released 14 Mar 2012.

Method: X-ray diffraction
Resolution: 3.05 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 4
Atoms: 6,120
Mol. weight: 104.02 kDa
Released: 14 Mar 2012

Explore 4D8P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4D8P contains 19 α-helices and 61 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	1
β-strand	19-26	8	1
β-strand	30-35	6	1
β-strand	40-43	4	1
α-helix	56-76	21
α-helix	81-83	3
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-128	3	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: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-26	4	1
β-strand	29-32	4	1
β-strand	35-40	6	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-87	7
β-strand	95	1	4
β-strand	98-103	6	5
β-strand	114-122	9	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	137-138	2	6
β-strand	143-144	2	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-162	8	5
β-strand	170-176	7	6
β-strand	184-189	6	6

Chain C: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	7
β-strand	19-26	8	7
β-strand	30-35	6	7
β-strand	40-43	4	7
β-strand	53	1	8
α-helix	56-76	21
α-helix	85-87	3
β-strand	88	1	9
β-strand	91-93	3	10
β-strand	103-112	10	10
β-strand	118-123	6	11
β-strand	126-127	2	11
β-strand	132-134	3	10
β-strand	138-140	3	10
β-strand	144-153	10	10
β-strand	161-166	6	11
β-strand	174-178	5	11

Chain D: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	-27	1	8
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	12
α-helix	96-97	2
β-strand	98	1	13
β-strand	101-103	3	14
β-strand	114-122	9	14
β-strand	123	1	12
β-strand	128-133	6	15
β-strand	137	1	15
β-strand	143-144	2	14
β-strand	148-149	2	14
β-strand	155-162	8	14
β-strand	170-176	7	15
β-strand	184-189	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA-DQA1 protein	A, C	protein	213	Homo sapiens	L8E864 (AlphaFold model)
Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain	B, D	protein	250	Triticum aestivum, Homo sapiens	Q5Y7D3 (AlphaFold model), Q94G94 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4D8P_1 HLA-DQA1 protein (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPEIPTPMSELTEGGGSGGGSCSRGGLEVLFQ

Sequence of entity 2 (B, D), FASTA

>4D8P_2 Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain (chains B, D)
RDSGPQPEQPEQPFPQPQGAGSLVPRGSGGGGSRDSPEDFVYQFKGMCYFTNGTERVRLV
SRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLEL
RTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPL
IRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKGGGSGGGSC
SRGGLEVLFQ

Primary citation

Structural and functional studies of trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) protein molecule. Tollefsen, S., Hotta, K., Chen, X. et al. J Biol Chem (2012) 287:13611-13619. DOI 10.1074/jbc.M111.320374 · PubMed

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