6U3M: DQ2-P.fluor-alpha1a

DQ2-P.fluor-alpha1a. Determined by X-ray diffraction at 1.9 Å resolution. Released 18 Dec 2019.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Pseudomonas fluorescens
Chains: 6
Atoms: 6,586
Mol. weight: 96.29 kDa
Ligands: PO4, NAG
Released: 18 Dec 2019

Explore 6U3M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U3M contains 28 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.

Chains A and C: 4 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	56-76	21
α-helix	81-85	5
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	118-123	6	9
β-strand	126-128	3	9
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	174-178	5	9

Chain B: 9 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	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-87	7
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
α-helix	165-166	2
β-strand	170-176	7	12
β-strand	184-189	6	12

Chain D: 9 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	47-49	3	1
α-helix	52-54	3
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	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	128-133	6	6
β-strand	136-138	3	6
β-strand	142-144	3	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-162	8	5
α-helix	165-166	2
β-strand	171-176	6	6
β-strand	184-188	5	6

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1-9	9

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1-6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, C	protein	191	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B, D	protein	206	Homo sapiens	O19712 (AlphaFold model)
Alpha1a peptide	E, F	protein	21	Pseudomonas fluorescens

Sequence of entity 1 (A, C), FASTA

>6U3M_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPETSGDDDDK

Sequence of entity 2 (B, D), FASTA

>6U3M_2 MHC class II HLA-DQ-beta-1 (chains B, D)
GGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLG
LPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNL
LVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCH
VEHPSLQSPITVEWRAQSTGGDDDDK

Sequence of entity 3 (E, F), FASTA

>6U3M_3 Alpha1a peptide (chains E, F)
AQPMPMPELPYPGSGGSIEGR

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease. Petersen, J., Ciacchi, L., Tran, M.T. et al. Nat Struct Mol Biol (2020) 27:49-61. DOI 10.1038/s41594-019-0353-4 · PubMed

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

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
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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