6XP6: 3C11-DQ2-glia-a2 complex

3C11-DQ2-glia-a2 complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 28 Jul 2021.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 10
Atoms: 13,695
Mol. weight: 192.98 kDa
Ligands: NAG, IPA
Released: 28 Jul 2021

Explore 6XP6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XP6 contains 66 α-helices and 142 β-strands across 10 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	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	126-128	3	3
β-strand	132-134	3	2
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: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
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	55-62	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	170-176	7	6
β-strand	184-189	6	6

Chains C and F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	10-12	3

Chain D: 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	81-87	7
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 E: 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	55-62	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	5
β-strand	114-122	9	5
β-strand	123	1	10
β-strand	128-133	6	11
β-strand	136-138	3	11
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	11
β-strand	184-188	5	11

Chain G: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	22
β-strand	10-13	4	23
β-strand	19-25	7	22
β-strand	39-44	6	23
β-strand	51-55	5	23
β-strand	66-67	2	23
α-helix	68	1
β-strand	76-83	6	22
β-strand	86-91	6	22
α-helix	96-98	3
β-strand	101-106	6	23
α-helix	112	1
β-strand	113-114	2	23
β-strand	118-122	5	23
β-strand	127	1	24
α-helix	128-129	2
β-strand	130-134	5	25
α-helix	135-137	3
α-helix	138-143	6
β-strand	145-155	11	25
β-strand	156	1	24
β-strand	160-166	7	26
β-strand	170	1	26
β-strand	175-179	5	25
α-helix	180-183	4
β-strand	189-198	10	25
α-helix	199-202	4
β-strand	207-214	8	26
β-strand	221-226	6	26

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	11-13	3	13
β-strand	19-26	8	12
α-helix	30-36	5
β-strand	38-44	7	13
β-strand	51-56	6	13
β-strand	66-67	2	13
α-helix	69-71	3
β-strand	76-81	6	12
α-helix	82-84	3
β-strand	86-91	6	12
α-helix	96-98	3
β-strand	100-107	8	13
β-strand	116-119	4	13
β-strand	123-127	5	13
α-helix	130-132	3
β-strand	133	1	14
α-helix	134-135	2
β-strand	136-140	5	15
β-strand	147-148	2	15
β-strand	151-161	11	15
β-strand	162	1	14
β-strand	167-170	4	16
α-helix	171-173	3
β-strand	175	1	16
β-strand	179-181	3	15
α-helix	182-184	3
β-strand	185-186	2	15
β-strand	192-201	10	15
α-helix	202-204	3
β-strand	210-216	7	16
α-helix	217-219	3
β-strand	221-227	7	16

Chain I: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10-13	4	28
β-strand	19-25	7	27
β-strand	39-44	6	28
β-strand	51-55	5	28
β-strand	66-67	2	28
α-helix	68	1
β-strand	76-83	6	27
β-strand	86-91	6	27
α-helix	96-98	3
β-strand	100-106	7	28
α-helix	112	1
β-strand	113-114	2	28
β-strand	118-122	5	28
β-strand	127	1	29
α-helix	128-129	2
β-strand	130-134	5	30
α-helix	135-137	3
α-helix	138-141	4
β-strand	145-155	11	30
β-strand	156	1	29
β-strand	160-166	7	31
β-strand	170	1	31
β-strand	175-179	5	30
α-helix	180-183	4
β-strand	189-198	10	30
α-helix	199-202	4
β-strand	207-214	8	31
β-strand	221-226	6	31

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II HLA-DQ-alpha chain	A, D	protein	191	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B, E	protein	201	Homo sapiens	Q5Y7D3 (AlphaFold model)
3.C11 IgH Fab	H, J	protein	224	Homo sapiens
3.C11 IgK Fab	G, I	protein	214	Homo sapiens
DQ2-glia-a2 peptide	C, F	protein	26	Triticum aestivum

Sequence of entity 1 (A, D), FASTA

>6XP6_1 MHC class II HLA-DQ-alpha chain (chains A, D)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPETSGDDDDK

Sequence of entity 2 (B, E), FASTA

>6XP6_2 MHC class II HLA-DQ-beta-1 (chains B, E)
SRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAE
YWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSV
TDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPS
LQSPITVEWRAQSTGGDDDDK

Sequence of entity 3 (H, J), FASTA

>6XP6_3 3.C11 IgH Fab (chains H, J)
QVQLVQSGAEVKKPGSSVKVSCKASGGTVRSRVHAISWVRQAPGQGLEWMGGIIPIFGTA
NYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARDVQRMGMDVWGQGTTVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 4 (G, I), FASTA

>6XP6_4 3.C11 IgK Fab (chains G, I)
DIQMTQSPSSVSTSVGDRVTITCRASQDISNWLAWYQQKPGKAPKLLIYDSSTLQSGVPS
RFSGSGSGTDFTLTISTLQPEDFATYYCQQFNSYPLTFGGGTKVDIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (C, F), FASTA

>6XP6_5 DQ2-glia-a2 peptide (chains C, F)
AAPQPELPYPQPGSGGSIEGRGGSGA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
IPA	Isopropyl alcohol	C3 H8 O	12

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

Primary citation

A high-affinity human TCR-like antibody detects celiac disease gluten peptide-MHC complexes and inhibits T cell activation. Frick, R., Hoydahl, L.S., Petersen, J. et al. Sci Immunol (2021) 6. DOI 10.1126/sciimmunol.abg4925 · 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
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
9EJH 2.45 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
6MFF 2.6 Å, HLA-DQ2-glia-omega1

Browse structure collections

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