9AUD: Immune receptor complex

Immune receptor complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 5 Feb 2025.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Mus musculus, Influenza A virus H3N2
Chains: 4
Atoms: 6,196
Mol. weight: 99.14 kDa
Ligands: NAG
Released: 5 Feb 2025

Explore 9AUD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AUD contains 20 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: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	11-14	4	8
β-strand	19-21	3	9
β-strand	23-26	4	7
β-strand	37-44	8	10
β-strand	51-56	6	10
β-strand	65-68	4	9
β-strand	76-79	4	9
β-strand	81	1	7
β-strand	86	1	7
β-strand	89-91	3	9
α-helix	96-98	3
β-strand	101-108	8	10
β-strand	118-119	2	10
β-strand	123-124	2	10
β-strand	125-128	4	8
β-strand	138-141	4	11
β-strand	150-154	5	11
β-strand	171-173	3	11
α-helix	174-176	3
β-strand	177	1	12
β-strand	190	1	12
β-strand	191-195	5	11

Chain B: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-21	3	15
β-strand	22-25	4	13
β-strand	38-44	7	14
β-strand	50-56	7	14
β-strand	66-71	6	15
β-strand	74-80	7	15
β-strand	86	1	13
β-strand	87-92	6	15
β-strand	100-107	8	14
β-strand	114-115	2	14
β-strand	119-124	6	14
α-helix	127-129	3
β-strand	131	1	16
β-strand	134-138	5	17
α-helix	139-141	3
α-helix	142-148	7
β-strand	150-160	11	17
β-strand	161	1	16
β-strand	165-171	7	18
β-strand	174-175	2	18
β-strand	180-182	3	17
β-strand	187-188	2	17
β-strand	198-207	10	17
α-helix	208-211	4
β-strand	217-224	8	18
β-strand	227	1	19
β-strand	241	1	19
β-strand	243-250	8	18

Chain C: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-17	12	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	42-45	4	1
α-helix	48-53	6
α-helix	58-76	19
α-helix	83-86	4
β-strand	90-95	6	2
β-strand	105-114	10	2
β-strand	120-125	6	3
β-strand	128-130	3	3
β-strand	134-136	3	2
β-strand	140-141	2	2
α-helix	142	1
β-strand	147-155	9	2
β-strand	163-168	6	3
β-strand	176-180	5	3

Chain D: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-20--14	7
β-strand	4-14	11	1
β-strand	21-29	9	1
β-strand	33-38	6	1
β-strand	43-46	4	1
α-helix	49-51	3
α-helix	52-60	9
α-helix	62-69	8
α-helix	71	1
α-helix	72-77	6
α-helix	78-81	4
α-helix	83-86	4
α-helix	88-90	3
β-strand	93	1	4
β-strand	96-98	3	5
β-strand	114-120	7	5
β-strand	121	1	4
β-strand	126-130	5	6
β-strand	134	1	6
β-strand	141-142	2	5
α-helix	143-145	3
β-strand	146-147	2	5
β-strand	153-158	6	5
β-strand	169-174	6	6
β-strand	182-186	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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 H3N2, Mus musculus	O92607, P14483 (AlphaFold model)
NPLCK1-2_TCR TRAV6-5 alpha chain	A	protein	210	Mus musculus
NPLCK1-2 TCR TRBV1 Beta chain	B	protein	242	Mus musculus

Sequence of entity 1 (C), FASTA

>9AUD_1 H-2 class II histocompatibility antigen, A-B alpha chain (chains C)
DIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQG
GLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVIN
ITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW
TSGLEVLF

Sequence of entity 2 (D), FASTA

>9AUD_2 Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain (chains D)
QVYSLIRPNENPAHKGSGGSIEGRGGSGASGDSERHFVYQFMGECYFTNGTQRIRYVTRY
IYNREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHT
SLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIR
NGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWTGGLEVLFQ

Sequence of entity 3 (A), FASTA

>9AUD_3 NPLCK1-2_TCR TRAV6-5 alpha chain (chains A)
MGDSVTQTEGPVTLSEGTSLTVNCSYETKQYPTLFWYVQYPGEGPQLLFKVPKANEKGSS
RGFEATYNKEATSFHLQKASVQESDSAVYYCALSLNSGGSNAKLTFGKGTKLSVKSHIQN
PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA
WSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (B), FASTA

>9AUD_4 NPLCK1-2 TCR TRBV1 Beta chain (chains B)
MVTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVK
SLPGADYLATRVTDTELRLQVANMSQGRTLYCTCSPQTTEVFFGKGTRLTVVEDLNKVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

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

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:

8VQ8 2.01 Å, Immune receptor complex
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
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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