6PY2: HLA-TCR complex

HLA-TCR complex. Determined by X-ray diffraction at 2.83 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 2.83 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 5
Atoms: 6,457
Mol. weight: 109.95 kDa
Ligands: NAG
Released: 15 Jan 2020

Explore 6PY2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PY2 contains 24 α-helices and 71 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: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	56-75	20
α-helix	80-86	7
β-strand	87-92	6	2
β-strand	102-111	10	2
β-strand	117-122	6	3
β-strand	125-127	3	3
β-strand	131-133	3	2
β-strand	137-138	2	2
β-strand	144-152	9	2
β-strand	160-165	6	3
β-strand	173-177	5	3

Chain B: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-31	9	1
β-strand	36-41	6	1
β-strand	47-49	3	1
α-helix	54-61	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
α-helix	96-97	2
β-strand	98-103	6	5
β-strand	115-122	8	5
β-strand	123	1	4
β-strand	128-132	5	6
β-strand	144	1	5
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	7-11	5

Chain D: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
β-strand	11-13	3	8
β-strand	19-21	3	9
β-strand	23-25	3	7
β-strand	33-38	6	8
α-helix	44	1
β-strand	45-50	6	8
β-strand	56-59	4	9
β-strand	62-65	4	9
β-strand	67	1	7
β-strand	72	1	7
β-strand	75-77	3	9
α-helix	82-84	3
β-strand	86-94	9	8
β-strand	99-102	4	8
β-strand	106-110	5	8
β-strand	120-125	6	10
β-strand	126	1	11
β-strand	133-138	6	10
β-strand	155-156	2	10
α-helix	157-159	3
β-strand	160-164	5	10
α-helix	165-167	3
β-strand	169-177	9	10
α-helix	185-188	4

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	12
β-strand	9-13	5	13
β-strand	18-23	6	12
α-helix	24	1
β-strand	30-36	7	13
α-helix	41-42	2
β-strand	43-48	6	13
β-strand	53-55	3	13
β-strand	64-67	4	12
β-strand	74-78	5	12
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	105-106	2	13
β-strand	110-115	6	13
α-helix	118-120	3
β-strand	122	1	14
α-helix	123-124	2
β-strand	125-129	5	11
α-helix	130-132	3
α-helix	133-138	6
β-strand	141-151	11	11
β-strand	152	1	14
β-strand	156-162	7	15
β-strand	165-166	2	15
β-strand	171-173	3	11
β-strand	178-179	2	11
β-strand	189-198	10	11
α-helix	199-202	4
β-strand	208-215	8	15
β-strand	218	1	16
α-helix	229-230	2
β-strand	232	1	16
β-strand	234-241	8	15

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, T594, alpha chain,T-cell receptor, T594, alpha chain	D	protein	206	Homo sapiens	K7N5N2 (AlphaFold model)
T-cell receptor, T594, beta chain,T-cell receptor, T594, beta chain	E	protein	245	Homo sapiens	K7N5M4

Sequence of entity 1 (A), FASTA

>6PY2_1 HLA class II histocompatibility antigen DQ alpha chain (chains A)
MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYV
DLERKETVWKLPLFHRLRFDPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKS
PVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLP
SADEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIR
GLRSVGASRHQGPL

Sequence of entity 2 (B), FASTA

>6PY2_2 HLA class II histocompatibility antigen DQ beta chain (chains B)
MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS
RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR
TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNGQEETAGVVSTPLI
RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVL
GLIFLGLGLIIHHRSQKGLLH

Sequence of entity 3 (C), FASTA

>6PY2_3 DQ2.2-glut-L1 (chains C)
APFSEQEQPVLG

Sequence of entity 4 (D), FASTA

>6PY2_4 T-cell receptor, T594, alpha chain,T-cell receptor, T594, alpha chain (chains D)
MNSVTQMEGPVTLSEEAFLTINCTYTATGYPSLFWYVQYPGEGLQLLLKATKADDKGSNK
GFEATYRKETTSFHLEKGSVQVSDSAVYFCASPQGGSEKLVFGKGTKLTVNPYIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6PY2_5 T-cell receptor, T594, beta chain,T-cell receptor, T594, beta chain (chains E)
MGVAQSPRYKIIEKRQSVAFWCNPISGHATLYWYQQILGQGPKLLIQFQNNGVVDDSQLP
KDRFSAERLKGVDSTLKIQPAKLEDSAVYLCASSSGGWGGGTEAFFGQGTRLTVVEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (GOL) are not listed.

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…
6PX6 3.0 Å, HLA-TCR complex

Browse structure collections

About this viewer

MolViewer shows 6PY2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.