5KSA: Bel602-DQ8.5-glia-gamma1 complex

Bel602-DQ8.5-glia-gamma1 complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 21 Sept 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 5
Atoms: 7,226
Mol. weight: 99.39 kDa
Ligands: NAG, CA
Released: 21 Sept 2016

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

Secondary structure: helices and β-sheets

5KSA contains 24 α-helices and 70 β-strands across 5 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	46-50	5
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	126-128	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: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
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	81-87	7
α-helix	90-92	3
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-103	6	5
β-strand	113-122	10	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-138	3	6
β-strand	142-144	3	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-163	9	5
β-strand	170-176	7	6
β-strand	184-189	6	6

Chain C: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	7
β-strand	16-20	5	8
β-strand	25-31	7	7
β-strand	36-44	9	8
β-strand	51-56	6	8
β-strand	65-68	4	7
β-strand	76-80	5	7
β-strand	86-91	6	7
α-helix	96-98	3
β-strand	100-108	9	8
β-strand	116-118	2	8
β-strand	122-127	6	8
β-strand	136-140	5	9
β-strand	141	1	10
β-strand	149-154	6	9
α-helix	163-165	3
β-strand	170-172	3	9
α-helix	173-175	3
β-strand	176-180	5	9
α-helix	181-183	3
β-strand	185-194	10	9

Chain D: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
α-helix	25-26	2
β-strand	38-45	8	12
β-strand	49-57	9	12
β-strand	64-68	5	12
β-strand	76-80	5	11
β-strand	87-91	5	11
α-helix	96-98	3
β-strand	100-107	8	12
β-strand	117-118	2	12
β-strand	122-127	6	12
α-helix	130-132	3
β-strand	134	1	13
α-helix	135-136	2
β-strand	137-141	5	14
β-strand	142	1	10
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	14
β-strand	164	1	13
β-strand	168-174	7	15
β-strand	177-179	3	15
β-strand	183-185	3	14
β-strand	190-191	2	14
β-strand	201-210	10	14
α-helix	211-214	4
β-strand	220-227	8	15
β-strand	230	1	16
α-helix	241-242	2
β-strand	244	1	16
β-strand	246-253	8	15

Chain J: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A	protein	191	Homo sapiens	P01909 (AlphaFold model)
HLA class II histocompatibility antigen, DQ beta 1 chain	B	protein	225	Triticum aestivum, Homo sapiens	A0A0U5Q247 (AlphaFold model), P08079 (AlphaFold model)
Bel602 alpha TRAV20*01	C	protein	206	Homo sapiens	A0A0B4J274 (AlphaFold model), P01848
Bel602 beta TRBV9*01	D	protein	243	Homo sapiens	A0A580, A0A5B9
DQ8.5-glia-gamma1 peptide	J	protein	11	Triticum aestivum	P08079 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5KSA_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPETSGDDDDK

Sequence of entity 2 (B), FASTA

>5KSA_2 HLA class II histocompatibility antigen, DQ beta 1 chain (chains B)
QPQQSFPEQEGSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNRE
EYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRV
EPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTF
QILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQSTGGDDDDK

Sequence of entity 3 (C), FASTA

>5KSA_3 Bel602 alpha TRAV20*01 (chains C)
MEDQVTQSPEALRLQEGESSSLNCSYTVSGLRGLFWYRQDPGKGPEFLFTLYSAGEEKEK
ERLKATLTKKESFLHITAPKPEDSATYLCAVQFMDSNYQLIWGAGTKLIIKPDIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>5KSA_4 Bel602 beta TRBV9*01 (chains D)
MGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNIL
ERFSAQQFPDLHSELNLSSLELGDSALYFCASSVAGTPSYEQYFGPGTRLTVTEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 5 (J), FASTA

>5KSA_5 DQ8.5-glia-gamma1 peptide (chains J)
QPQQSFPEQEA

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

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
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
6MFF 2.6 Å, HLA-DQ2-glia-omega1

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