8VQ8: Immune receptor complex

Immune receptor complex. Determined by X-ray diffraction at 2.01 Å resolution. Released 29 Jan 2025.

Method: X-ray diffraction
Resolution: 2.01 Å
Organisms: Mus musculus, Influenza A virus
Chains: 4
Atoms: 6,625
Mol. weight: 99.32 kDa
Ligands: NAG
Released: 29 Jan 2025

Explore 8VQ8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VQ8 contains 28 α-helices and 68 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: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	11-14	4	2
β-strand	19-21	3	3
β-strand	23-26	4	1
β-strand	38-44	7	2
β-strand	51-56	6	2
β-strand	65-68	4	3
β-strand	76-79	4	3
β-strand	81	1	1
β-strand	86	1	1
β-strand	89-91	3	3
α-helix	96-98	3
β-strand	100-107	8	2
β-strand	115-117	3	2
β-strand	121-126	6	2
α-helix	127-128	2
β-strand	135-138	4	4
α-helix	139-142	4
β-strand	148-153	6	4
α-helix	162-164	3
β-strand	169-171	3	4
α-helix	172-174	3
β-strand	175-179	5	4
α-helix	180-182	3
β-strand	184-193	10	4
α-helix	200-203	4
β-strand	214	1	4

Chain B: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	5
β-strand	10-13	4	2
β-strand	19-25	7	5
β-strand	38-44	7	2
β-strand	50-55	6	2
β-strand	66-71	6	5
β-strand	74-83	9	5
β-strand	86-92	7	5
β-strand	100-107	8	2
α-helix	115	1
β-strand	116-117	2	2
β-strand	121-125	5	2
α-helix	129-131	3
β-strand	133	1	6
α-helix	134-135	2
β-strand	136-140	5	7
α-helix	141-143	3
α-helix	144-150	7
β-strand	152-162	11	7
β-strand	163	1	6
β-strand	167-173	7	8
β-strand	176-178	3	8
β-strand	182-184	3	7
α-helix	188	1
β-strand	189-190	2	7
β-strand	200-209	10	7
α-helix	210-214	5
β-strand	219-226	8	8
α-helix	240-241	2
β-strand	245-252	8	8

Chain C: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-17	12	9
β-strand	21-28	8	9
β-strand	31-37	7	9
β-strand	42-45	4	9
α-helix	48-53	6
β-strand	55	1	10
α-helix	59-78	20
α-helix	81-87	7
β-strand	90-95	6	11
β-strand	105-114	10	11
β-strand	120-125	6	12
β-strand	128-130	3	12
β-strand	134-136	3	11
α-helix	137-139	3
β-strand	140-141	2	11
β-strand	147-155	9	11
β-strand	162-168	7	12
β-strand	176-181	6	12

Chain D: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	-24	1	10
β-strand	4-15	12	9
β-strand	20-29	10	9
β-strand	32-38	7	9
β-strand	43-46	4	9
α-helix	49-51	3
α-helix	52-60	9
α-helix	62-71	10
α-helix	72-77	6
α-helix	78-81	4
α-helix	83-86	4
α-helix	88-90	3
β-strand	93	1	13
α-helix	94-95	2
β-strand	96	1	14
β-strand	118	1	14
β-strand	120	1	15
β-strand	121	1	13
α-helix	143-145	3
β-strand	146-147	2	15
β-strand	153-154	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T cell receptor - LCK1-1 TRAV6-5 alpha chain	A	protein	207	Mus musculus
T cell receptor - LCK1-1 TRBV1 Beta chain	B	protein	243	Mus musculus
H-2 class II histocompatibility antigen, A-B alpha chain	C	protein	188	Mus musculus	P14434 (AlphaFold model)
Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain	D	protein	228	Influenza A virus, Mus musculus	P14483 (AlphaFold model), P69296

Sequence of entity 1 (A), FASTA

>8VQ8_1 T cell receptor - LCK1-1 TRAV6-5 alpha chain (chains A)
GDSVTQTEGPVTLSEGTSLTVNCSYETKQYPTLFWYVQYPGEGPQLLFKVPKANEKGSSR
GFEATYNKEATSFHLQKASVQESDSAVYYCALRISSGSWQLIFGSGTQLTVMPHIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>8VQ8_2 T cell receptor - LCK1-1 TRBV1 Beta chain (chains B)
VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKS
LPGADYLATRVTDTELRLQVANMSQGRTLYCTCSAELGGDTQYFGPGTRLLVLEDLNKVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 3 (C), FASTA

>8VQ8_3 H-2 class II histocompatibility antigen, A-B alpha chain (chains C)
DIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQG
GLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVIN
ITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW
TSGLEVLF

Sequence of entity 4 (D), FASTA

>8VQ8_4 Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain (chains D)
QVYSLIRPNENPAHKGSGGSIEGRGGSGASGDSERHFVYQFMGECYFTNGTQRIRYVTRY
IYNREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHT
SLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIR
NGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWTGGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

LCK-co-receptor association ensures T cell lineage fidelity and maximizes epitope-specific TCR diversity. Zhang, J.B., Chaurasia, P., Nguyen, A. et al. Sci Immunol (2025) 10:eadp5016-eadp5016. DOI 10.1126/sciimmunol.adp5016 · PubMed

Other PDB entries of the same protein (UniProt P14434 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RAL 2.1 Å, CL3E peptide bound to the I-Ab murine MHC class II receptor
1MUJ 2.15 Å, Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide
4P23 2.25 Å, J809.B5 TCR bound to IAb/3K
1LNU 2.5 Å, Crystal structure of class II MHC molecule iab bound to EALPHA3K peptide
3C5Z 2.55 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506
6MNG 2.66 Å, 4738 TCR bound to IAb Padi4
3RDT 2.7 Å, Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide
6MNN 2.83 Å, 6236 TCR bound to I-Ab Padi4
4P46 2.85 Å, J809.B5 Y31A TCR bound to IAb3K
6MNO 2.9 Å, 6235 TCR bound to I-Ab Padi4
9AUD 2.9 Å, Immune receptor complex
3C60 3.05 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR YAe62

Browse structure collections

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