4GG6: Protein complex

Protein complex. Determined by X-ray diffraction at 3.2 Å resolution. Released 24 Oct 2012.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 10
Atoms: 11,919
Mol. weight: 198.84 kDa
Ligands: NAG
Released: 24 Oct 2012

Explore 4GG6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GG6 contains 42 α-helices and 138 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: 5 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	46-51	6
α-helix	56-76	21
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
α-helix	128	1
β-strand	132-134	3	2
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	161-166	6	3
α-helix	173	1
β-strand	174-178	5	3

Chain B: 6 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	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	4
β-strand	98-103	6	5
β-strand	115-120	6	5
β-strand	123	1	4
β-strand	128-131	4	6
β-strand	142-144	3	5
β-strand	148-149	2	7
β-strand	155-156	2	7
β-strand	157-161	5	5
β-strand	173-176	4	6
α-helix	183	1
β-strand	184-186	3	6

Chain C: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	8
β-strand	19-26	8	8
β-strand	29-35	7	8
β-strand	40-43	4	8
α-helix	46-51	6
β-strand	53	1	9
α-helix	56-76	21
α-helix	81-85	5
β-strand	88-93	6	10
β-strand	103-112	10	10
β-strand	118-123	6	11
β-strand	126-127	2	11
α-helix	128	1
β-strand	132-134	3	10
β-strand	138-139	2	10
β-strand	145-153	9	10
β-strand	161-166	6	11
α-helix	173	1
β-strand	174-178	5	11

Chain D: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	8
β-strand	23-32	10	8
β-strand	35-41	7	8
β-strand	47-49	3	8
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
β-strand	98-103	6	13
β-strand	115-122	8	13
β-strand	123	1	12
β-strand	128-131	4	14
β-strand	142-144	3	13
α-helix	145-147	3
β-strand	148-149	2	13
β-strand	155-161	7	13
β-strand	171-176	6	14
β-strand	184-188	5	14

Chain E: 2 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
β-strand	37-44	8	16
β-strand	50-56	7	16
β-strand	65-67	3	15
β-strand	77-80	4	15
β-strand	86-91	6	15
α-helix	96-98	3
β-strand	100-108	9	16
β-strand	118	1	16
β-strand	122-127	6	16
β-strand	136-142	7	17
β-strand	149-154	6	17
β-strand	171-172	2	17
α-helix	173-176	4
β-strand	177-178	2	17
β-strand	189-193	5	17
β-strand	215	1	17

Chains F and H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	18
β-strand	10-14	5	16
β-strand	19-24	6	18
β-strand	38-45	8	16
β-strand	49-57	9	16
β-strand	64-68	5	16
β-strand	76-80	5	18
β-strand	87-91	5	18
α-helix	96-98	3
β-strand	100-107	8	16
β-strand	117-118	2	16
β-strand	122-127	6	16
α-helix	130-132	3
β-strand	134	1	19
β-strand	137-142	6	17
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	17
β-strand	164	1	19
β-strand	168-174	7	20
β-strand	177-179	3	20
β-strand	183-185	3	17
β-strand	190-191	2	17
β-strand	201-210	10	17
α-helix	211-214	4
β-strand	220-227	8	20
β-strand	230	1	21
α-helix	241-242	2
β-strand	244	1	21
β-strand	246-253	8	20

Chain G: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	22
β-strand	10-14	5	23
β-strand	19-24	6	22
β-strand	37-44	8	23
β-strand	50-56	7	23
β-strand	65-67	3	22
β-strand	77-80	4	22
β-strand	86-91	6	22
α-helix	96-98	3
β-strand	100-108	9	23
β-strand	118	1	23
β-strand	122-127	6	23
β-strand	136-142	7	24
β-strand	149-154	6	24
β-strand	171-172	2	24
α-helix	173-176	4
β-strand	177-178	2	24
β-strand	189-193	5	24

Chain I: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	9
α-helix	3-4	2
α-helix	8-12	5

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
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, C	protein	192	Homo sapiens	P01909 (AlphaFold model)
HLA class II histocompatibility antigen, DQ beta 1 chain	B, D	protein	215	Homo sapiens	P01920 (AlphaFold model)
T-cell receptor, SP3.4 alpha chain	E, G	protein	207	Homo sapiens	K7N5N2 (AlphaFold model)
T-cell receptor, SP3.4 beta chain	F, H	protein	245	Homo sapiens	P01850 (AlphaFold model)
Peptide from Alpha/beta-gliadin MM1	I, J	protein	18	Triticum aestivum	P18573

Sequence of entity 1 (A, C), FASTA

>4GG6_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPESSADLVPR

Sequence of entity 2 (B, D), FASTA

>4GG6_2 HLA class II histocompatibility antigen, DQ beta 1 chain (chains B, D)
GGGGSIEGRGSGGGSRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVG
VYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSR
TEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTP
QRGDVYTCHVEHPSLQNPIIVEWRAQSSSADLVPR

Sequence of entity 3 (E, G), FASTA

>4GG6_3 T-CELL RECEPTOR, SP3.4 ALPHA CHAIN (chains E, G)
MDAKTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRM
ASLAIAEDRKSSTLILHRATLRDAAVYYCILRDGRGGADGLTFGKGTHLIIQPYIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>4GG6_4 T-CELL RECEPTOR, SP3.4 BETA CHAIN (chains F, H)
DSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNI
LERFSAQQFPDLHSELNLSSLELGDSALYFCASSVAVSAGTYEQYFGPGTRLTVTEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Sequence of entity 5 (I, J), FASTA

>4GG6_5 Peptide from Alpha/beta-gliadin MM1 (chains I, J)
QQYPSGEGSFQPSQENPQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Biased T cell receptor usage directed against human leukocyte antigen DQ8-restricted gliadin peptides is associated with celiac disease. Broughton, S.E., Petersen, J., Theodossis, A. et al. Immunity (2012) 37:611-621. DOI 10.1016/j.immuni.2012.07.013 · 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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