6XCP: Immune receptor complex

Immune receptor complex. Determined by X-ray diffraction at 3.3 Å resolution. Released 14 Jul 2021.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,351
Mol. weight: 98.47 kDa
Ligands: NAG, PO4
Released: 14 Jul 2021

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

Secondary structure: helices and β-sheets

6XCP contains 18 α-helices and 75 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: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	1
β-strand	11-14	4	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-49	4
β-strand	54	1	2
α-helix	57-76	20
α-helix	80-83	4
β-strand	88-93	6	3
β-strand	103-110	8	3
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	132-134	3	3
α-helix	135-137	3
β-strand	138-139	2	5
β-strand	145-146	2	5
β-strand	147-153	7	3
β-strand	161-166	6	4
β-strand	174-177	4	4

Chain C: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	-1-0	2
β-strand	1	1	2
α-helix	7-9	3
β-strand	35-44	10	1
β-strand	45	1	6
β-strand	48	1	6
β-strand	52-59	8	1
β-strand	62-68	7	1
β-strand	74-76	3	1
α-helix	82-90	9
α-helix	92-101	10
α-helix	102-106	5
α-helix	107-115	9
α-helix	117-119	3
β-strand	122	1	7
β-strand	125-130	6	8
β-strand	141-147	7	8
β-strand	150	1	7
β-strand	155-160	6	9
β-strand	163-165	3	9
β-strand	169-171	3	8
α-helix	172-174	3
β-strand	175-176	2	8
β-strand	182-189	8	8
β-strand	197-203	7	9
β-strand	211-216	6	9

Chain D: 1 helix, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	10
β-strand	10-14	5	11
β-strand	19-24	6	10
β-strand	38-44	7	11
β-strand	51-56	6	11
β-strand	66-67	2	10
β-strand	77-80	4	10
β-strand	86-91	6	10
β-strand	101-107	7	11
β-strand	120-125	6	11
β-strand	134-140	7	12
β-strand	147-152	6	12
α-helix	162-164	3
β-strand	165	1	12
β-strand	168-170	3	12
β-strand	175-178	4	13
β-strand	183-186	4	13
β-strand	187-192	6	12

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	14
β-strand	10-14	5	15
β-strand	19-24	6	14
β-strand	38-45	8	15
β-strand	49-56	8	15
β-strand	65-68	4	15
β-strand	76-80	5	14
β-strand	87-91	5	14
α-helix	96-98	3
β-strand	101-107	7	15
β-strand	113-115	3	15
β-strand	119-124	6	15
β-strand	131	1	16
β-strand	134-139	6	12
α-helix	140-141	2
α-helix	142-147	6
β-strand	150-160	11	12
β-strand	161	1	16
β-strand	165-171	7	17
β-strand	174-175	2	17
β-strand	180-182	3	12
β-strand	187-188	2	12
β-strand	198-207	10	12
α-helix	208-211	4
β-strand	217-224	8	17
β-strand	227	1	18
α-helix	238-239	2
β-strand	241	1	18
β-strand	243-250	8	17

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-DQ8-beta chain fusion	C	protein	230	Homo sapiens	O19707 (AlphaFold model)
T-CELL-RECEPTOR, A2.13-alpha chain	D	protein	203	Homo sapiens
T-CELL-RECEPTOR, A2.13-beta chain	E	protein	240	Homo sapiens

Sequence of entity 1 (A), FASTA

>6XCP_1 MHC class II HLA-DQ-alpha chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPESTGGDDDDK

Sequence of entity 2 (C), FASTA

>6XCP_2 Hybrid insulin peptide, MHC class II HLA-DQ8-beta chain fusion (chains C)
GQVELGGGNAVEVCKGSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVTRY
IYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTT
LQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRN
GDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQSTGGDDDDK

Sequence of entity 3 (D), FASTA

>6XCP_3 T-CELL-RECEPTOR, A2.13-alpha chain (chains D)
MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMAS
LIITEDRKSSTLILPHATLRDTAVYYCIVSHNAGNMLTFGGGTRLMVKPHIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E), FASTA

>6XCP_4 T-CELL-RECEPTOR, A2.13-beta chain (chains E)
MGVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFP
GRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLERETQYFGPGTRLLVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
PO4	Phosphate ion	O4 P	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
6XCO 2.9 Å, Immune receptor complex
8VD2 2.9 Å, Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1

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