6XC9: Immune receptor complex

Immune receptor complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 14 Jul 2021.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,543
Mol. weight: 200.51 kDa
Ligands: NAG
Released: 14 Jul 2021

Explore 6XC9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XC9 contains 51 α-helices and 153 β-strands across 8 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.

Chains A and F: 4 helices, 14 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	46-51	6
β-strand	53-54	2	2
α-helix	56-76	21
α-helix	81-85	5
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	132-134	3	3
α-helix	137	1
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-178	5	4

Chain C: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	-1	1
β-strand	0-1	2	2
α-helix	4-6	3
β-strand	7	1	5
α-helix	8-9	2
α-helix	18-19	2
β-strand	22-32	11	1
β-strand	37-46	10	1
β-strand	49-55	7	1
β-strand	61-63	3	1
α-helix	69-77	9
α-helix	79-88	10
α-helix	89-94	6
α-helix	95-102	8
α-helix	104-106	3
β-strand	109	1	6
α-helix	110-111	2
β-strand	112-117	6	7
β-strand	129-136	8	7
β-strand	137	1	6
β-strand	142-147	6	8
β-strand	151	1	8
β-strand	156-158	3	7
α-helix	159-161	3
β-strand	162-163	2	7
β-strand	169-175	7	7
β-strand	184-190	7	8
β-strand	198-203	6	8

Chain D: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	10-14	5	10
β-strand	19-21	3	9
β-strand	24-25	2	9
β-strand	29	1	2
β-strand	37-44	8	10
β-strand	51-57	7	10
α-helix	65-66	2
β-strand	67-68	2	9
β-strand	76-81	6	9
β-strand	86-91	6	9
α-helix	96-98	3
β-strand	100-108	9	10
β-strand	114-116	3	10
β-strand	120-125	6	10
β-strand	134-139	6	11
β-strand	140	1	12
β-strand	147-152	6	11
β-strand	169-170	2	11
α-helix	171-173	3
β-strand	174-178	5	11
β-strand	183-191	9	11
α-helix	199-202	4
β-strand	213	1	11

Chain E: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	14
β-strand	19-24	6	13
β-strand	38-45	8	14
β-strand	49-57	9	14
β-strand	64-68	5	14
β-strand	76-80	5	13
β-strand	87-91	5	13
α-helix	96-98	3
β-strand	100-107	8	14
β-strand	111	1	5
β-strand	119-120	2	14
β-strand	124-129	6	14
β-strand	136	1	15
α-helix	137-138	2
β-strand	139-143	5	12
α-helix	144-146	3
α-helix	147-153	7
β-strand	155-165	11	12
β-strand	166	1	15
β-strand	170-176	7	16
β-strand	179-181	3	16
β-strand	185-187	3	12
α-helix	191	1
β-strand	192-193	2	12
β-strand	203-212	10	12
α-helix	213-216	4
β-strand	222-229	8	16
β-strand	232	1	17
β-strand	246	1	17
β-strand	248-255	8	16

Chain H: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	-1	1
β-strand	0-1	2	19
α-helix	4-6	3
β-strand	7	1	22
α-helix	8-9	2
β-strand	22-32	11	18
β-strand	37-46	10	18
β-strand	49-55	7	18
β-strand	61-63	3	18
α-helix	69-77	9
α-helix	79-88	10
α-helix	89-94	6
α-helix	95-102	8
α-helix	104-106	3
β-strand	109	1	23
α-helix	110-111	2
β-strand	112-116	5	24
β-strand	128-136	9	24
β-strand	137	1	23
β-strand	142-147	6	25
β-strand	150-152	3	25
β-strand	156-158	3	24
α-helix	159-161	3
β-strand	162-163	2	24
β-strand	169-176	8	24
β-strand	184-190	7	25
β-strand	198-203	6	25

Chain I: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	26
β-strand	10-14	5	27
β-strand	19-21	3	26
β-strand	24-25	2	26
β-strand	29	1	19
β-strand	37-44	8	27
β-strand	51-57	7	27
α-helix	65-66	2
β-strand	67-68	2	26
β-strand	76-81	6	26
β-strand	86-91	6	26
α-helix	96-98	3
β-strand	100-108	9	27
β-strand	114-116	3	27
β-strand	120-125	6	27
β-strand	134-139	6	28
β-strand	140	1	29
β-strand	147-152	6	28
β-strand	164	1	28
β-strand	169-170	2	28
α-helix	171-173	3
β-strand	174-178	5	28
β-strand	183-191	9	28
α-helix	199-203	5
α-helix	209-211	3
β-strand	213	1	28

Chain J: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	30
β-strand	10-14	5	31
β-strand	19-24	6	30
α-helix	25	1
β-strand	38-45	8	31
β-strand	49-57	9	31
β-strand	64-68	5	31
β-strand	76-80	5	30
β-strand	87-91	5	30
α-helix	96-98	3
β-strand	100-107	8	31
β-strand	111	1	22
β-strand	119-120	2	31
β-strand	124-129	6	31
β-strand	136	1	32
α-helix	137-138	2
β-strand	139-143	5	29
α-helix	144-146	3
α-helix	147-153	7
β-strand	155-165	11	29
β-strand	166	1	32
β-strand	170-176	7	33
β-strand	179-181	3	33
β-strand	185-187	3	29
α-helix	191	1
β-strand	192-193	2	29
β-strand	203-212	10	29
α-helix	213-216	4
β-strand	222-229	8	33
β-strand	232	1	34
β-strand	246	1	34
β-strand	248-255	8	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II HLA-DQ-alpha chain	A, F	protein	193	Homo sapiens	Q30069 (AlphaFold model)
Hybrid Insulin Peptide, MHC class II HLA-DQ-beta chain fusion	C, H	protein	230	Homo sapiens	O19707 (AlphaFold model)
T-CELL-RECEPTOR, A3.10-alpha chain	D, I	protein	208	Homo sapiens
T-CELL-RECEPTOR, A3.10-beta chain	E, J	protein	245	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>6XC9_1 MHC class II HLA-DQ-alpha chain (chains A, F)
EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ
FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV
NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH
WEPESTGGDDDDK

Sequence of entity 2 (C, H), FASTA

>6XC9_2 Hybrid Insulin Peptide, MHC class II HLA-DQ-beta chain fusion (chains C, H)
GQVELGGGNAVEVCKGSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVTRY
IYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTT
LQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRN
GDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQSTGGDDDDK

Sequence of entity 3 (D, I), FASTA

>6XC9_3 T-CELL-RECEPTOR, A3.10-alpha chain (chains D, I)
MQTVTQSQPEMSVQEAETVTLSCTYDTSESNYYLFWYKQPPSRQMILVIRQEAYKQQNAT
ENRFSVNFQKAAKSFSLKISDSQLGDTAMYFCAFFGQGAQKLVFGQGTRLTINPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E, J), FASTA

>6XC9_4 T-CELL-RECEPTOR, A3.10-beta chain (chains E, J)
MGVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFP
GRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLSASGGATDTQYFGPGTRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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
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
6XCP 3.3 Å, Immune receptor complex

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