6PX6: HLA-TCR complex

HLA-TCR complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 5
Atoms: 6,291
Mol. weight: 111.41 kDa
Released: 15 Jan 2020

Explore 6PX6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PX6 contains 23 α-helices and 69 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: 4 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	56-76	21
α-helix	81-83	3
α-helix	85-87	3
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	127	1	3
β-strand	132-134	3	2
β-strand	138-139	2	2
α-helix	140	1
β-strand	145-153	9	2
β-strand	161-166	6	3
β-strand	174-178	5	3

Chain B: 7 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	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
α-helix	90-92	3
β-strand	95	1	4
β-strand	98-103	6	5
β-strand	115-122	8	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	155-161	7	5
β-strand	171-176	6	6
β-strand	184-188	5	6

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3

Chain D: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
β-strand	10-14	5	8
β-strand	19-25	7	7
β-strand	32-39	8	8
β-strand	43-51	9	8
β-strand	56-59	4	7
β-strand	62-65	4	7
β-strand	67	1	7
β-strand	69-74	6	7
α-helix	79-81	3
β-strand	84-90	7	8
β-strand	95-97	3	8
β-strand	101-106	6	8
α-helix	107-108	2
β-strand	115-121	7	9
β-strand	128-133	6	9
β-strand	150-151	2	9
α-helix	152-154	3
β-strand	155-158	4	9
β-strand	165-172	8	9

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	10
β-strand	10-13	4	11
β-strand	19-24	6	10
β-strand	31-37	7	11
β-strand	44-50	7	11
β-strand	53-56	4	11
β-strand	65-68	4	10
β-strand	75-79	5	10
α-helix	84-86	3
β-strand	88-95	8	11
β-strand	104-105	2	11
β-strand	109-113	5	11
α-helix	117-119	3
β-strand	121	1	12
α-helix	122-123	2
β-strand	124-129	6	9
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-150	11	9
β-strand	151	1	12
β-strand	155-161	7	13
β-strand	164-165	2	13
α-helix	166	1
β-strand	170-172	3	9
β-strand	177-178	2	9
β-strand	188-197	10	9
α-helix	198-201	4
β-strand	207-214	8	13
β-strand	217	1	14
α-helix	228-229	2
β-strand	231	1	14
β-strand	233-240	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen DQ alpha chain	A	protein	254	Homo sapiens	Q08AS3 (AlphaFold model)
HLA class II histocompatibility antigen DQ beta chain	B	protein	261	Homo sapiens	A0A0U5IHY9 (AlphaFold model)
DQ2.2-glut-L1	C	protein	12	Triticum aestivum	P16315 (AlphaFold model)
T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain	D	protein	217	Homo sapiens	K7N5M3 (AlphaFold model)
T-cell receptor, T1005.2.56, beta chain	E	protein	256	Homo sapiens

Sequence of entity 1 (A), FASTA

>6PX6_1 HLA class II histocompatibility antigen DQ alpha chain (chains A)
MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYV
DLERKETVWKLPLFHRLRFDPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKS
PVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLP
SADEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIR
GLRSVGASRHQGPL

Sequence of entity 2 (B), FASTA

>6PX6_2 HLA class II histocompatibility antigen DQ beta chain (chains B)
MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS
RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR
TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNGQEETAGVVSTPLI
RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVL
GLIFLGLGLIIHHRSQKGLLH

Sequence of entity 3 (C), FASTA

>6PX6_3 DQ2.2-glut-L1 (chains C)
APFSEQEQPVLG

Sequence of entity 4 (D), FASTA

>6PX6_4 T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain (chains D)
MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTS
GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVHTGARLMFGDGTQLVVKPNIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESSKLAAALEHHHHH

Sequence of entity 5 (E), FASTA

>6PX6_5 T-cell receptor, T1005.2.56, beta chain (chains E)
MGVSQTPSNKVTEKGKYVELRCDPISGHTALYWYRQSLGQGPEFLIYFQGTGAADDSGLP
NDRFFAVRPEGSVSTLKIQRTERGDSAVYLCASSHGASTDTQYFGPGTRLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RADKLAAALEHHHHHH

Primary citation

A molecular basis for the T cell response in HLA-DQ2.2 mediated celiac disease. Ting, Y.T., Dahal-Koirala, S., Kim, H.S.K. et al. Proc Natl Acad Sci U S A (2020) 117:3063-3073. DOI 10.1073/pnas.1914308117 · PubMed

Other PDB entries of the same protein (UniProt Q08AS3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EJI 2.2 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
9RUG 2.74 Å, Cryo-EM structure of the LB_DQB0303_A Fab - HLA-DQB1*03:03/DQA1*02:01 human…
6PY2 2.83 Å, HLA-TCR complex

Browse structure collections

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