4OZG: D2 protein complex

D2 protein complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 10
Atoms: 12,715
Mol. weight: 194.86 kDa
Ligands: NAG, CA
Released: 16 Apr 2014

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

Secondary structure: helices and β-sheets

4OZG contains 48 α-helices and 144 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: 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	48-50	3
α-helix	56-77	22
α-helix	81-85	5
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: 7 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	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-87	7
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
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: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	7
β-strand	20-26	7	7
β-strand	29-35	7	7
β-strand	40-43	4	7
α-helix	47-50	4
α-helix	56-76	21
α-helix	81-84	4
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	117	1	9
β-strand	120-123	4	10
β-strand	127	1	10
β-strand	132-134	3	8
β-strand	138-139	2	8
β-strand	145-153	9	8
β-strand	156	1	11
β-strand	159	1	11
β-strand	161-164	4	10
β-strand	167	1	9
β-strand	176-178	3	10

Chain D: 5 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	55-61	7
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-87	7
β-strand	95	1	12
β-strand	98-103	6	13
β-strand	114-122	9	13
β-strand	123	1	12
β-strand	128-133	6	14
β-strand	136-138	3	14
β-strand	142-144	3	13
β-strand	148-149	2	13
β-strand	155-162	8	13
β-strand	170-176	7	14
β-strand	184-189	6	14

Chain E: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	15
β-strand	10-14	5	16
β-strand	19-24	6	15
α-helix	37	1
β-strand	38-44	7	16
α-helix	49-50	2
β-strand	51-56	6	16
β-strand	66-67	2	15
β-strand	77-80	4	15
β-strand	86-91	6	15
α-helix	96-98	3
β-strand	100-107	8	16
β-strand	122-127	6	16
β-strand	136-140	5	17
α-helix	141	1
β-strand	142	1	18
β-strand	150-154	5	17
β-strand	170-172	3	17
α-helix	173-175	3
β-strand	176-180	5	17
β-strand	185-194	10	17
β-strand	215	1	17

Chain F: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	19
β-strand	10-14	5	20
β-strand	19-24	6	19
β-strand	38-44	7	20
β-strand	46	1	21
β-strand	48	1	21
β-strand	50-57	8	20
β-strand	64	1	20
β-strand	76-79	4	19
β-strand	87-91	5	19
α-helix	96-98	3
β-strand	100-106	7	20
α-helix	115-116	2
β-strand	117-118	2	20
β-strand	122-127	6	20
α-helix	130-132	3
β-strand	134	1	22
β-strand	137-141	5	18
α-helix	142-144	3
α-helix	145-151	7
β-strand	153-163	11	18
β-strand	164	1	22
β-strand	167-174	8	23
β-strand	177-179	3	23
β-strand	183-185	3	18
β-strand	190-191	2	18
β-strand	201-210	10	18
α-helix	211-214	4
β-strand	220-228	9	23
β-strand	230	1	24
α-helix	241-242	2
β-strand	244	1	24
β-strand	246-253	8	23

Chain G: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	25
β-strand	10-14	5	26
α-helix	18	1
β-strand	19-24	6	25
β-strand	38-44	7	26
β-strand	51-56	6	26
β-strand	66-67	2	25
β-strand	77-80	4	25
β-strand	86-91	6	25
α-helix	96-98	3
β-strand	100-107	8	26
β-strand	122-127	6	26
α-helix	128-129	2
β-strand	136-140	5	27
β-strand	141-142	2	28
β-strand	150-156	7	27
β-strand	171-172	2	27
α-helix	173-175	3
β-strand	176-180	5	27
β-strand	185-193	9	27
α-helix	201-204	4
β-strand	215	1	27

Chain H: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	29
β-strand	10-14	5	30
β-strand	19-24	6	29
β-strand	38-45	8	30
β-strand	49-57	9	30
β-strand	64	1	30
β-strand	76-79	4	29
β-strand	87-91	5	29
α-helix	96-98	3
β-strand	100-107	8	30
α-helix	115-116	2
β-strand	117-118	2	30
β-strand	122-127	6	30
α-helix	130-132	3
β-strand	134	1	31
β-strand	137-142	6	28
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	28
β-strand	164	1	31
β-strand	168-174	7	32
β-strand	177-179	3	32
β-strand	183-185	3	28
α-helix	189	1
β-strand	190-191	2	28
β-strand	201-210	10	28
α-helix	211-215	5
β-strand	220-227	8	32
β-strand	230	1	33
α-helix	241-242	2
β-strand	244	1	33
β-strand	246-253	8	32

2 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
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, C	protein	191	Homo sapiens	P01909 (AlphaFold model)
HLA class II histocompatibility antigen, DQ beta 1 chain	B, D	protein	213	Homo sapiens	P01920 (AlphaFold model)
T-cell receptor, d2, alpha chain	E, G	protein	202	Homo sapiens	Q2YD82 (AlphaFold model)
T-cell receptor, d2, beta chain	F, H	protein	242	Homo sapiens	P01850 (AlphaFold model)
deamidated Gliadin-alpha2 peptide	I, J	protein	13	Triticum aestivum	P04722

Sequence of entity 1 (A, C), FASTA

>4OZG_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPETSGDDDDK

Sequence of entity 2 (B, D), FASTA

>4OZG_2 HLA class II histocompatibility antigen, DQ beta 1 chain (chains B, D)
GGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEF
RAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTE
ALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQR
GDVYTCHVEHPSLQSPITVEWRAQSTGGDDDDK

Sequence of entity 3 (E, G), FASTA

>4OZG_3 T-cell receptor, d2, alpha chain (chains E, G)
MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMAS
LIITEDRKSSTLILPHATLRDTAVYYCIVLGGADGLTFGKGTHLIIQPYIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>4OZG_4 T-cell receptor, d2, beta chain (chains F, H)
MGVSQSPSNKVTEKGKDVELRCDPISGHTALYWYRQSLGQGLEFLIYFQGNSAPDKSGLP
SDRFSAERTGGSVSTLTIQRTQQEDSAVYLCASSFRFTDTQYFGPGTRLTVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Sequence of entity 5 (I, J), FASTA

>4OZG_5 deamidated Gliadin-alpha2 peptide (chains I, J)
APQPELPYPQPGS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
CA	Calcium ion	Ca	1

Primary citation

T-cell receptor recognition of HLA-DQ2-gliadin complexes associated with celiac disease. Petersen, J., Montserrat, V., Mujico, J.R. et al. Nat Struct Mol Biol (2014) 21:480-488. DOI 10.1038/nsmb.2817 · 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
6XP6 2.4 Å, 3C11-DQ2-glia-a2 complex
9EJH 2.45 Å, Peptide-independent T cell receptor recognition of HLA-DQ2

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