4Z7U: S13 complex

S13 complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 3 Jun 2015.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 10
Atoms: 13,076
Mol. weight: 198.82 kDa
Ligands: NAG
Released: 3 Jun 2015

Explore 4Z7U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Z7U contains 54 α-helices and 140 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, 14 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
β-strand	53	1	2
α-helix	57-76	20
α-helix	81-87	7
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	132-134	3	3
α-helix	137	1
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-178	5	4

Chain B: 6 helices, 14 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	46-49	4	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	5
β-strand	98-102	5	6
β-strand	115-122	8	6
β-strand	123	1	5
β-strand	128-130	3	7
β-strand	143-144	2	6
α-helix	145-147	3
β-strand	148-149	2	6
β-strand	155-161	7	6
β-strand	171-176	6	7
β-strand	184-188	5	7

Chain C: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	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	57-76	20
α-helix	81-87	7
β-strand	88-93	6	10
β-strand	103-112	10	10
β-strand	118-123	6	11
β-strand	126-128	3	11
β-strand	132-134	3	10
α-helix	137	1
β-strand	138-139	2	10
β-strand	145-153	9	10
β-strand	161-166	6	11
β-strand	174-178	5	11

Chain D: 7 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	128-130	3	14
β-strand	143-144	2	13
α-helix	145-147	3
β-strand	148-149	2	13
β-strand	155-161	7	13
α-helix	169-170	2
β-strand	171-176	6	14
β-strand	184-188	5	14

Chain E: 8 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	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
α-helix	114-116	3
β-strand	122-127	6	16
α-helix	128-129	2
β-strand	136-141	6	17
β-strand	142	1	18
β-strand	149-154	6	17
α-helix	163-165	3
β-strand	170-172	3	17
α-helix	173-175	3
β-strand	176-180	5	17
α-helix	181-183	3
β-strand	185-194	10	17
α-helix	201-203	3
β-strand	215	1	17

Chain F: 6 helices, 24 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	38-45	8	20
β-strand	49-57	9	20
β-strand	64-68	5	20
β-strand	76-80	5	19
β-strand	87-91	5	19
α-helix	96-98	3
β-strand	100-107	8	20
β-strand	117-118	2	20
β-strand	122-127	6	20
α-helix	130-132	3
β-strand	134	1	21
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	21
β-strand	168-174	7	22
β-strand	177-178	2	22
β-strand	183-185	3	18
α-helix	189	1
β-strand	190-191	2	18
β-strand	201-210	10	18
α-helix	211-214	4
β-strand	220-227	8	22
β-strand	230	1	23
β-strand	244	1	23
β-strand	246-253	8	22

Chain G: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	24
β-strand	10-14	5	25
β-strand	19-24	6	24
β-strand	38-44	7	25
α-helix	49-50	2
β-strand	51-56	6	25
β-strand	66-67	2	24
β-strand	77-80	4	24
β-strand	86-91	6	24
α-helix	96-98	3
β-strand	100-107	8	25
α-helix	114-116	3
β-strand	122-127	6	25
β-strand	136-141	6	26
β-strand	142	1	27
β-strand	149-154	6	26
α-helix	163-165	3
β-strand	170-172	3	26
α-helix	173-175	3
β-strand	176-180	5	26
α-helix	181-183	3
β-strand	185-194	10	26
α-helix	201-203	3
β-strand	215	1	26

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	28
β-strand	10-14	5	29
β-strand	19-24	6	28
β-strand	38-45	8	29
β-strand	49-57	9	29
β-strand	64-68	5	29
β-strand	76-80	5	28
β-strand	87-91	5	28
α-helix	96-98	3
β-strand	100-107	8	29
β-strand	117-118	2	29
β-strand	122-127	6	29
α-helix	130-132	3
β-strand	134	1	30
β-strand	137-141	5	27
α-helix	142-144	3
α-helix	145-151	7
β-strand	153-163	11	27
β-strand	164	1	30
β-strand	168-174	7	31
β-strand	177-179	3	31
β-strand	183-185	3	27
α-helix	189	1
β-strand	190-191	2	27
β-strand	201-210	10	27
α-helix	211-214	4
β-strand	220-227	8	31
β-strand	230	1	32
β-strand	244	1	32
β-strand	246-253	8	31

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
MHC class II HLA-DQ-alpha chain	A, C	protein	192	Homo sapiens	Q30069 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B, D	protein	213	Homo sapiens	P01920 (AlphaFold model)
T-cell receptor, S13 alpha chain	E, G	protein	203	Homo sapiens	K7N5N2 (AlphaFold model)
T-cell receptor, S13 beta chain	F, H	protein	245	Homo sapiens	P01850 (AlphaFold model)
deamidated DQ8-glia-alpha1 peptide	I, J	protein	18	Triticum aestivum	P18573

Sequence of entity 1 (A, C), FASTA

>4Z7U_1 MHC class II HLA-DQ-alpha chain (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPETSGDDDDK

Sequence of entity 2 (B, D), FASTA

>4Z7U_2 MHC class II HLA-DQ-beta-1 (chains B, D)
GGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVY
RAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTE
ALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQR
GDVYTCHVEHPSLQNPIIVEWRAQSTGGDDDDK

Sequence of entity 3 (E, G), FASTA

>4Z7U_3 T-CELL RECEPTOR, S13 ALPHA CHAIN (chains E, G)
DAKTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRMA
SLAIAEDRKSSTLILHRATLRDAAVYYCILRDRSNQFYFGTGTSLTVIPNIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>4Z7U_4 T-CELL RECEPTOR, S13 BETA CHAIN (chains F, H)
DSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNI
LERFSAQQFPDLHSELNLSSLELGDSALYFCASSTTPGTGTETQYFGPGTRLLVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Sequence of entity 5 (I, J), FASTA

>4Z7U_5 deamidated DQ8-glia-alpha1 peptide (chains I, J)
APSGEGSFQPSQENPQGS

Ligands and cofactors

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

Primary citation

Determinants of Gliadin-Specific T Cell Selection in Celiac Disease. Petersen, J., van Bergen, J., Loh, K.L. et al. J Immunol (2015) 194:6112-6122. DOI 10.4049/jimmunol.1500161 · PubMed

Other PDB entries of the same protein (UniProt Q30069 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DFX 2.03 Å, human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide
6XC9 2.4 Å, Immune receptor complex
8VD0 2.4 Å, Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2
5KS9 2.55 Å, Bel502-DQ8-glia-alpha1 complex
8VCX 2.59 Å, Human TCR A2.13 in complex with DQ8-InsCpep
8VCY 2.6 Å, Human TCR A2.13 in complex with DQ8-InsC8-15NPY
8VDD 2.6 Å, Crystal structure of Proinsulin C-peptide bound to HLA-DQ8
4Z7V 2.65 Å, L3-12 complex
4Z7W 2.89 Å, T316 complex
6XCO 2.9 Å, Immune receptor complex
8VD2 2.9 Å, Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1
6XCP 3.3 Å, Immune receptor complex

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