9NIG: PB TCR

PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide. Determined by X-ray diffraction at 3.2 Å resolution. Released 21 May 2025.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 15
Atoms: 18,764
Mol. weight: 289.11 kDa
Ligands: NAG
Released: 21 May 2025

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

Secondary structure: helices and β-sheets

9NIG contains 68 α-helices and 223 β-strands across 15 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: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	48-51	4
α-helix	58-76	19
α-helix	80-84	5
β-strand	85	1	2
β-strand	88-93	6	3
β-strand	98	1	4
β-strand	101	1	4
β-strand	103-112	10	3
β-strand	113	1	2
β-strand	118-123	6	5
β-strand	126-128	3	5
β-strand	133-134	2	3
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	5
β-strand	174-178	5	5

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-79	5
α-helix	80-85	6
β-strand	95	1	6
β-strand	98-104	7	7
β-strand	114-122	9	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-137	2	8
β-strand	142-143	2	7
β-strand	148-149	2	7
β-strand	155-162	8	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain C: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	18
β-strand	19-26	8	18
β-strand	29-35	7	18
β-strand	40-43	4	18
α-helix	46-49	4
β-strand	53	1	19
α-helix	58-76	19
α-helix	81-83	3
β-strand	85	1	20
β-strand	90-93	4	21
β-strand	103-108	6	21
β-strand	109-112	4	22
β-strand	113	1	20
β-strand	118-123	6	23
β-strand	133-134	2	21
α-helix	136-137	2
β-strand	138-139	2	22
β-strand	145-147	3	22
β-strand	149-153	5	21
β-strand	161-166	6	23
β-strand	176-178	3	23

Chain D: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2
β-strand	7-18	12	18
β-strand	23-32	10	18
β-strand	35-41	7	18
β-strand	47-49	3	18
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-79	5
α-helix	80-85	6
β-strand	95	1	24
β-strand	98-104	7	25
β-strand	114-122	9	25
β-strand	123	1	24
β-strand	128-133	6	26
β-strand	136-137	2	26
β-strand	142-143	2	25
β-strand	148-149	2	25
β-strand	155-162	8	25
α-helix	165-166	2
β-strand	170-176	7	26
β-strand	184-189	6	26

Chain E: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10-14	5	28
β-strand	19-21	3	29
β-strand	22-25	4	27
β-strand	38-44	7	28
β-strand	50-56	7	28
β-strand	65-68	4	29
β-strand	76-80	5	29
β-strand	86	1	27
β-strand	87-91	5	29
α-helix	96-98	3
β-strand	100-107	8	28
α-helix	109-114	6
β-strand	118-119	2	28
β-strand	123-128	6	28
β-strand	137-142	6	30
β-strand	143	1	31
β-strand	150-155	6	30
α-helix	164-166	3
β-strand	171-173	3	30
β-strand	177-181	5	30
α-helix	182-184	3
β-strand	186-195	10	30
β-strand	216	1	30

Chain F: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	32
β-strand	10-14	5	33
β-strand	19-21	3	34
β-strand	22-24	3	32
β-strand	38-45	8	33
β-strand	49-58	10	33
β-strand	65-68	4	33
β-strand	76-78	3	34
β-strand	86	1	32
β-strand	89-91	3	34
α-helix	96-98	3
β-strand	100-107	8	33
β-strand	114-115	2	33
β-strand	119-124	6	33
α-helix	127-129	3
β-strand	131	1	35
β-strand	134-138	5	31
α-helix	139-141	3
α-helix	142-148	7
β-strand	150-160	11	31
β-strand	161	1	35
β-strand	165-171	7	36
β-strand	174-175	2	36
β-strand	180-182	3	31
β-strand	187-188	2	31
α-helix	196-197	2
β-strand	198-207	10	31
α-helix	208-212	5
β-strand	217-224	8	36
β-strand	227	1	37
α-helix	238-239	2
β-strand	241	1	37
β-strand	243-250	8	36

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1014	1	19
α-helix	1019-1022	4

Chain H: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	38
β-strand	19-26	8	38
β-strand	29-35	7	38
β-strand	40-43	4	38
α-helix	46-50	5
α-helix	59-76	18
α-helix	80-84	5
β-strand	85	1	39
α-helix	86-87	2
β-strand	90-93	4	40
β-strand	103-112	10	40
β-strand	113	1	39
β-strand	118-123	6	41
β-strand	126-127	2	41
α-helix	128	1
β-strand	133-134	2	40
β-strand	138-139	2	40
β-strand	145-153	9	40
β-strand	161-166	6	41
β-strand	174-178	5	41

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, C, H	protein	189	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen DR beta chain	B, D, I	protein	190	Homo sapiens	A0A1V1IGJ9 (AlphaFold model)
PB TCR alpha chain	E, J, M	protein	208	Homo sapiens
PB TCR beta chain	F, K, N	protein	239	Homo sapiens
Tenascin	G, L, P	protein	14	Homo sapiens	P24821 (AlphaFold model)

Sequence of entity 1 (A, C, H), FASTA

>9NIG_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, C, H)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DTSGDDDDK

Sequence of entity 2 (B, D, I), FASTA

>9NIG_2 HLA class II histocompatibility antigen DR beta chain (chains B, D, I)
DTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEYW
NSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVNG
FYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSLT
SPLTVEWRAT

Sequence of entity 3 (E, J, M), FASTA

>9NIG_3 PB TCR alpha chain (chains E, J, M)
MQQLNQSPQSMFIQEGEDVSMNCTSSSIFNTWLWYKQEPGEGPVLLIALYKAGELTSNGR
LTAQFGITRKDSFLNISASIPSDVGIYFCAGQDVGNTNAGKSTFGDGTTLTVKPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, K, N), FASTA

>9NIG_4 PB TCR beta chain (chains F, K, N)
GITQSPRYKITETGRQVTLMCHQTWSHSYMFWYRQDLGHGLRLIYYSAAADITDKGEVPD
GYVVSRSKTENFPLTLESATRSQTSVYFCASSGVPPVQFFGPGTRLTVLEDLNKVFPPEV
AVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALND
SRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Sequence of entity 5 (G, L, P), FASTA

>9NIG_5 Tenascin (chains G, L, P)
DRYRLNYSLPTGKK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

Primary citation

The molecular basis of T cell receptor recognition of citrullinated tenascin-C presented by HLA-DR4. Dao, H.T., Loh, T.J., Sharma, R.K. et al. J Biol Chem (2025) 301:110326-110326. DOI 10.1016/j.jbc.2025.110326 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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