6XCO: Immune receptor complex

Immune receptor complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 14 Jul 2021.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,447
Mol. weight: 99.16 kDa
Ligands: NAG, CAC
Released: 14 Jul 2021

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

Secondary structure: helices and β-sheets

6XCO contains 22 α-helices and 71 β-strands across 4 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: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	1
β-strand	19-21	3	1
β-strand	23-26	4	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
β-strand	53-54	2	2
α-helix	57-76	20
α-helix	81-84	4
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-127	2	4
α-helix	128	1
β-strand	132-134	3	3
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
α-helix	173	1
β-strand	174-178	5	4

Chain B: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	0-1	2	2
α-helix	46-47	2
β-strand	50-60	11	1
β-strand	65-74	10	1
β-strand	77-83	7	1
β-strand	89-91	3	1
α-helix	97-105	9
α-helix	107-116	10
α-helix	117-122	6
α-helix	123-130	8
α-helix	132-134	3
β-strand	137	1	5
α-helix	138-139	2
β-strand	140-145	6	6
β-strand	157-164	8	6
β-strand	165	1	5
β-strand	170-175	6	7
β-strand	179-180	2	7
β-strand	184-186	3	6
β-strand	190-191	2	6
β-strand	197-203	7	6
β-strand	213-218	6	7
β-strand	226-228	3	7

Chain D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	36-44	9	9
α-helix	49-50	2
β-strand	51-56	6	9
β-strand	65-68	4	8
β-strand	76-80	5	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	101-108	8	9
β-strand	115-116	2	9
β-strand	120-125	6	9
β-strand	134-137	4	10
α-helix	138-141	4
β-strand	147-152	6	10
β-strand	169-170	2	10
α-helix	174	1
β-strand	175-176	2	11
α-helix	177	1
β-strand	187-192	6	10

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
β-strand	38-45	8	13
β-strand	49-57	9	13
β-strand	64-68	5	13
β-strand	76-80	5	12
β-strand	87-91	5	12
α-helix	96-98	3
β-strand	100-107	8	13
β-strand	113-115	3	13
β-strand	119-124	6	13
α-helix	127-129	3
β-strand	131	1	14
β-strand	134-138	5	11
α-helix	139-141	3
α-helix	142-148	7
β-strand	150-160	11	11
β-strand	161	1	14
β-strand	165-171	7	15
β-strand	174-176	3	15
β-strand	180-182	3	11
β-strand	187-188	2	11
β-strand	198-207	10	11
α-helix	208-211	4
β-strand	217-224	8	15
β-strand	227	1	16
β-strand	241	1	16
β-strand	243-250	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II HLA-DQ-alpha chain	A	protein	193	Homo sapiens	Q30069 (AlphaFold model)
Hybrid Insulin Peptide, MHC class II HLA-DQ-beta-1 fusion	B	protein	230	Homo sapiens	O19707 (AlphaFold model)
T-CELL-RECEPTOR, A1.9-alpha chain	D	protein	205	Homo sapiens
T-CELL-RECEPTOR, A1.9-beta chain	E	protein	240	Homo sapiens

Sequence of entity 1 (A), FASTA

>6XCO_1 MHC class II HLA-DQ-alpha chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPESTGGDDDDK

Sequence of entity 2 (B), FASTA

>6XCO_2 Hybrid Insulin Peptide, MHC class II HLA-DQ-beta-1 fusion (chains B)
GQVELGGGNAVEVCKGSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVTRY
IYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTT
LQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRN
GDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQSTGGDDDDK

Sequence of entity 3 (D), FASTA

>6XCO_3 T-CELL-RECEPTOR, A1.9-alpha chain (chains D)
MEDQVTQSPEALRLQEGESSSLNCSYTVSGLRGLFWYRQDPGKGPEFLFTLYSAGEEKEK
ERLKATLTKKESFLHITAPKPEDSATYLCAVQAGGNNRLAFGKGNQVVVIPNIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E), FASTA

>6XCO_4 T-CELL-RECEPTOR, A1.9-beta chain (chains E)
MGVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFP
GRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLERDGYTFGSGTRLTVVEDLNKVFPPE
VAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
CAC	Cacodylate ion	C2 H6 As O2	1

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

Primary citation

T cell receptor recognition of hybrid insulin peptides bound to HLA-DQ8. Tran, M.T., Faridi, P., Lim, J.J. et al. Nat Commun (2021) 12:5110-5110. DOI 10.1038/s41467-021-25404-x · 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
5KS9 2.55 Å, Bel502-DQ8-glia-alpha1 complex
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
8VD2 2.9 Å, Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1
6XCP 3.3 Å, Immune receptor complex

Browse structure collections

About this viewer

MolViewer shows 6XCO 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.