5KSB: T15-DQ8.5-glia-gamma1 complex

T15-DQ8.5-glia-gamma1 complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 21 Sept 2016.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 10
Atoms: 13,106
Mol. weight: 199.43 kDa
Ligands: NAG
Released: 21 Sept 2016

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

Secondary structure: helices and β-sheets

5KSB contains 52 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	48-50	3
α-helix	57-76	20
α-helix	81-84	4
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: 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	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	4
β-strand	98-102	5	5
β-strand	115-122	8	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-137	2	6
β-strand	142-144	3	5
α-helix	145-146	2
β-strand	148-149	2	5
β-strand	155-161	7	5
β-strand	171-176	6	6
β-strand	184-188	5	6

Chain C: 3 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	46-48	3
α-helix	57-76	20
α-helix	80-87	8
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
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 D: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
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	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	10
β-strand	98-102	5	11
β-strand	115-122	8	11
β-strand	123	1	10
β-strand	128-133	6	12
β-strand	136-137	2	12
β-strand	143-144	2	11
α-helix	145-147	3
β-strand	148-149	2	11
β-strand	155-161	7	11
β-strand	171-176	6	12
β-strand	184-188	5	12

Chain E: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	36-44	9	14
β-strand	51-56	6	14
β-strand	65-68	4	13
β-strand	76-80	5	13
β-strand	86-91	6	13
α-helix	96-98	3
β-strand	100-108	9	14
α-helix	109-111	3
β-strand	117-118	2	14
β-strand	122-127	6	14
β-strand	136-139	4	15
α-helix	140	1
β-strand	141	1	16
α-helix	142-143	2
β-strand	149-154	6	15
β-strand	170-172	3	15
α-helix	173-175	3
β-strand	176-180	5	15
β-strand	185-194	10	15
α-helix	201-203	3
β-strand	215	1	15

Chain F: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	17
β-strand	10-14	5	18
β-strand	19-24	6	17
β-strand	38-45	8	18
β-strand	49-57	9	18
β-strand	64-68	5	18
β-strand	76-80	5	17
β-strand	87-91	5	17
α-helix	96-98	3
β-strand	100-107	8	18
α-helix	114-116	3
β-strand	117-118	2	18
β-strand	122-127	6	18
α-helix	130-132	3
β-strand	134	1	19
β-strand	137-141	5	20
β-strand	142	1	16
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	20
β-strand	164	1	19
β-strand	168-174	7	21
β-strand	177-179	3	21
β-strand	183-185	3	20
α-helix	189	1
β-strand	190-191	2	20
α-helix	199-200	2
β-strand	201-210	10	20
α-helix	211-215	5
β-strand	220-227	8	21
β-strand	230	1	22
α-helix	241-242	2
β-strand	244	1	22
β-strand	246-253	8	21

Chain G: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	10-14	5	24
β-strand	19-25	7	23
β-strand	36-44	9	24
α-helix	49-50	2
β-strand	51-56	6	24
β-strand	65-68	4	23
β-strand	76-80	5	23
β-strand	86-91	6	23
α-helix	96-98	3
β-strand	101-108	8	24
β-strand	117-118	2	24
β-strand	122-127	6	24
α-helix	128-129	2
β-strand	136-139	4	25
α-helix	140	1
β-strand	141	1	26
α-helix	142-143	2
β-strand	149-156	8	25
β-strand	170-172	3	25
α-helix	173-175	3
β-strand	176-180	5	25
β-strand	185-194	10	25
α-helix	201-203	3
β-strand	215	1	25

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	27
β-strand	10-14	5	28
β-strand	19-24	6	27
β-strand	38-45	8	28
β-strand	49-57	9	28
β-strand	64-68	5	28
β-strand	76-80	5	27
β-strand	87-91	5	27
α-helix	96-98	3
β-strand	101-107	7	28
α-helix	114-116	3
β-strand	117-118	2	28
β-strand	122-127	6	28
α-helix	130-132	3
β-strand	134	1	29
β-strand	137-141	5	30
β-strand	142	1	26
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	30
β-strand	164	1	29
β-strand	168-174	7	31
β-strand	177-179	3	31
β-strand	183-185	3	30
α-helix	189	1
β-strand	190-191	2	30
β-strand	201-210	10	30
α-helix	211-215	5
β-strand	220-227	8	31
β-strand	230	1	32
α-helix	241-242	2
β-strand	244	1	32
β-strand	246-253	8	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
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	225	Triticum aestivum, Homo sapiens	A0A0U5Q247 (AlphaFold model), P08079 (AlphaFold model)
T15 TCR alpha TRAV20*02	E, G	protein	206	Homo sapiens	A0A0B4J274 (AlphaFold model), P01848
T15 TCR beta TRBV9*01	F, H	protein	243	Homo sapiens	A0A580, A0A5B9
DQ8.5-glia-gamma1 peptide	I, J	protein	11	Triticum aestivum	P08079 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5KSB_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPETSGDDDDK

Sequence of entity 2 (B, D), FASTA

>5KSB_2 HLA class II histocompatibility antigen, DQ beta 1 chain (chains B, D)
QPQQSFPEQEGSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNRE
EYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRV
EPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTF
QILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQSTGGDDDDK

Sequence of entity 3 (E, G), FASTA

>5KSB_3 T15 TCR alpha TRAV20*02 (chains E, G)
MEDQVTQSPEALRLQEGESSSLNCSYTVSGLRGLFWYRQDPGKGPEFLFTLYSAGEEKEK
ERLKATLTKKESFLHITAPKPEDSATYLCAVQASGGSYIPTFGRGTSLIVHPYIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>5KSB_4 T15 TCR beta TRBV9*01 (chains F, H)
MGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNIL
ERFSAQQFPDLHSELNLSSLELGDSALYFCASSNRGLGTDTQYFGPGTRLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 5 (I, J), FASTA

>5KSB_5 DQ8.5-glia-gamma1 peptide (chains I, J)
GPQQSFPEQEA

Ligands and cofactors

ID	Name	Formula	Copies
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 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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