5KS9: Bel502-DQ8-glia-alpha1 complex

Bel502-DQ8-glia-alpha1 complex. Determined by X-ray diffraction at 2.55 Å resolution. Released 21 Sept 2016.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 10
Atoms: 13,515
Mol. weight: 200.96 kDa
Ligands: CA, NAG
Released: 21 Sept 2016

Explore 5KS9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KS9 contains 54 α-helices and 148 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, 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	52-53	2	2
α-helix	56-76	21
α-helix	80-85	6
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
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, 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	81-86	6
β-strand	95	1	5
β-strand	98-102	5	6
β-strand	115-122	8	6
β-strand	123	1	5
β-strand	128-133	6	7
β-strand	136-137	2	7
β-strand	142-144	3	6
α-helix	145-147	3
β-strand	148-149	2	6
β-strand	155-161	7	6
β-strand	170-176	7	7
β-strand	184-189	6	7
α-helix	190-191	2

Chain C: 3 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	48-51	4
β-strand	52-53	2	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	126-128	3	11
β-strand	132-134	3	10
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: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
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
α-helix	96-97	2
β-strand	98-102	5	13
β-strand	115-122	8	13
β-strand	123	1	12
β-strand	128-133	6	14
β-strand	136-137	2	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: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	15
β-strand	16-20	5	16
β-strand	25-31	7	15
β-strand	36-44	9	16
α-helix	49-50	2
β-strand	51-56	6	16
β-strand	65-68	4	15
β-strand	76-80	5	15
β-strand	86-91	6	15
α-helix	96-98	3
β-strand	100-108	9	16
β-strand	117-118	2	16
β-strand	122-127	6	16
α-helix	128-129	2
β-strand	136-139	4	17
α-helix	140	1
β-strand	141	1	18
α-helix	142-143	2
β-strand	149-156	8	17
β-strand	161-162	2	19
α-helix	163-165	3
β-strand	170-172	3	17
β-strand	176-180	5	17
β-strand	185-194	10	17
β-strand	209-210	2	19

Chain F: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	20
β-strand	10-14	5	21
β-strand	19-24	6	20
β-strand	38-45	8	21
β-strand	49-57	9	21
β-strand	64-68	5	21
β-strand	76-80	5	20
β-strand	87-91	5	20
α-helix	96-98	3
β-strand	100-107	8	21
α-helix	114-116	3
β-strand	117-118	2	21
β-strand	122-127	6	21
α-helix	130-132	3
β-strand	134	1	22
α-helix	135-136	2
β-strand	137-141	5	23
β-strand	142	1	18
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	23
β-strand	164	1	22
β-strand	168-174	7	24
β-strand	177-179	3	24
β-strand	183-185	3	23
α-helix	189	1
β-strand	190-191	2	23
β-strand	201-210	10	23
α-helix	211-214	4
β-strand	220-227	8	24
β-strand	230	1	25
α-helix	241-242	2
β-strand	244	1	25
β-strand	246-253	8	24

Chain G: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	26
β-strand	16-20	5	27
β-strand	25-31	7	26
β-strand	36-44	9	27
α-helix	49-50	2
β-strand	51-56	6	27
β-strand	65-68	4	26
β-strand	76-80	5	26
β-strand	86-91	6	26
α-helix	96-98	3
β-strand	100-108	9	27
β-strand	117-118	2	27
β-strand	122-127	6	27
β-strand	136-139	4	28
α-helix	140	1
β-strand	141	1	29
α-helix	142-143	2
β-strand	149-154	6	28
β-strand	162	1	30
α-helix	163-165	3
β-strand	171-172	2	28
α-helix	173-175	3
β-strand	176-180	5	28
β-strand	185-194	10	28
β-strand	209	1	30

Chain H: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	31
β-strand	10-14	5	32
β-strand	19-24	6	31
α-helix	25-26	2
β-strand	38-45	8	32
β-strand	49-57	9	32
β-strand	64-68	5	32
β-strand	76-80	5	31
β-strand	87-91	5	31
α-helix	96-98	3
β-strand	100-107	8	32
α-helix	114-116	3
β-strand	117-118	2	32
β-strand	122-127	6	32
β-strand	134	1	33
β-strand	137-141	5	34
β-strand	142	1	29
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	34
β-strand	164	1	33
β-strand	168-174	7	35
β-strand	177-179	3	35
β-strand	183-185	3	34
α-helix	189	1
β-strand	190-191	2	34
β-strand	201-210	10	34
α-helix	211-214	4
β-strand	220-227	8	35
β-strand	230	1	36
β-strand	244	1	36
β-strand	246-253	8	35

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	192	Homo sapiens	Q30069 (AlphaFold model)
HLA class II histocompatibility antigen, DQ beta 1 chain	B, D	protein	230	Triticum aestivum, Homo sapiens	P01920 (AlphaFold model)
Bel502 TCR alpha TRAV20*01	E, G	protein	207	Homo sapiens	P01848 (AlphaFold model)
Bel502 TCR beta TRBV9*01	F, H	protein	242	Homo sapiens	P01850 (AlphaFold model)
DQ8-glia-alpha1 peptide	I, J	protein	16	Triticum aestivum	P18573

Sequence of entity 1 (A, C), FASTA

>5KS9_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPETSGDDDDK

Sequence of entity 2 (B, D), FASTA

>5KS9_2 HLA class II histocompatibility antigen, DQ beta 1 chain (chains B, D)
PSGEGSFQPSQENPQGSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVTRY
IYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTT
LQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRN
GDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQSTGGDDDDK

Sequence of entity 3 (E, G), FASTA

>5KS9_3 Bel502 TCR alpha TRAV20*01 (chains E, G)
MEDQVTQSPEALRLQEGESSSLNCSYTVSGLRGLFWYRQDPGKGPEFLFTLYSAGEEKEK
ERLKATLTKKESFLHITAPKPEDSATYLCAVALNNNAGNMLTFGGGTRLMVKPHIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>5KS9_4 Bel502 TCR beta TRBV9*01 (chains F, H)
MGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNIL
ERFSAQQFPDLHSELNLSSLELGDSALYFCASSVAPGSDTQYFGPGTRLTVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Sequence of entity 5 (I, J), FASTA

>5KS9_5 DQ8-glia-alpha1 peptide (chains I, J)
APSGEGSFQPSQENPQ

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Diverse T Cell Receptor Gene Usage in HLA-DQ8-Associated Celiac Disease Converges into a Consensus Binding Solution. Petersen, J., Kooy-Winkelaar, Y., Loh, K.L. et al. Structure (2016) 24:1643-1657. DOI 10.1016/j.str.2016.07.010 · 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
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
4Z7U 2.7 Å, S13 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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