7N5P: 6218 TCR

6218 TCR in complex with H2-Db PA224-233 with a cysteine mutant. Determined by X-ray diffraction at 2.09 Å resolution. Released 20 Jul 2022.

Method: X-ray diffraction
Resolution: 2.09 Å
Organisms: Mus musculus, Homo sapiens, Influenza A virus
Chains: 5
Atoms: 6,808
Mol. weight: 95.39 kDa
Released: 20 Jul 2022

Explore 7N5P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N5P contains 20 α-helices and 70 β-strands across 5 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	227-228	2
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4
α-helix	274-276	3

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5

Chain D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	10-14	5	9
β-strand	19-24	6	8
β-strand	32-44	8	9
α-helix	49-50	2
β-strand	51-56	6	9
β-strand	67-68	2	8
β-strand	80-83	4	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-108	9	9
β-strand	120-125	6	9
β-strand	134-140	7	10
β-strand	147-152	6	10
β-strand	168-170	3	10
α-helix	171-173	3
β-strand	174-178	5	10
β-strand	183-192	10	10
β-strand	213	1	10

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
β-strand	31-44	7	12
β-strand	50-58	9	12
β-strand	61-68	4	12
β-strand	77-79	3	11
β-strand	86-91	6	11
α-helix	96-98	3
β-strand	100-107	8	12
β-strand	113-114	2	12
β-strand	118-123	6	12
β-strand	130	1	13
α-helix	131-132	2
β-strand	133-138	6	10
α-helix	139-140	2
α-helix	141-147	7
β-strand	149-159	11	10
β-strand	160	1	13
β-strand	164-170	7	14
β-strand	173-175	3	14
β-strand	179-181	3	10
β-strand	186-187	2	10
β-strand	197-206	10	10
α-helix	207-211	5
β-strand	216-223	8	14
β-strand	226	1	15
β-strand	240	1	15
β-strand	242-249	8	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A	protein	277	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
peptide from Polymerase acidic protein	C	protein	10	Influenza A virus	O89752
Fusion protein of T cell receptor alpha variable 21-DV12 and T-cell receptor, sp3.4 alpha chain	D	protein	204	Mus musculus, Homo sapiens	A0A075B6C4 (AlphaFold model), K7N5N2
Fusion protein of T cell receptor beta, variable 29 and Human nkt tcr beta chain	E	protein	240	Mus musculus, Homo sapiens	A0A0G2LB96, K7N5M4

Sequence of entity 1 (A), FASTA

>7N5P_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPP

Sequence of entity 2 (B), FASTA

>7N5P_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7N5P_3 peptide from Polymerase acidic protein (chains C)
SSLCNFRAYV

Sequence of entity 4 (D), FASTA

>7N5P_4 Fusion protein of T cell receptor alpha variable 21-DV12 and T-cell receptor, sp3.4 alpha chain (chains D)
DAKTTQPDSMESTEGETVHLPCSHATISGNEYIYWYRQVPLQGPEYVTHGLQQNTTNSMA
FLAIASDRKSSTLILPHVSLRDAAVYHCILSGGSNYKLTFGKGTLLTVTPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>7N5P_5 Fusion protein of T cell receptor beta, variable 29 and Human nkt tcr beta chain (chains E)
DMKVTQMPRYLIKRMGENVLLECGQDMSHETMYWYRQDPGLGLQLIYISYDVDSNSEGDI
PKGYRVSRKKREHFSLILDSAKTNQTSVYFCASSFGREQYFGPGTRLTVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Primary citation

Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus. Szeto, C., Zareie, P., Wirasinha, R.C. et al. Nat Commun (2022) 13:4951-4951. DOI 10.1038/s41467-022-32692-4 · PubMed

Other PDB entries of the same protein (UniProt P01899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WZY 1.5 Å, Structure of DbNA(10) peptides bound to H-2Db MHC-I
6X00 1.55 Å, Structure of DbNA(11) peptides bound to H-2Db MHC-I
7N9J 1.74 Å, Crystal structure of H2DB in complex with HSF2 melanoma neoantigen
5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
7N5Q 1.76 Å, Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
1WBX 1.9 Å, Crystal structures of murine MHC class I H-2 db and kb molecules in complex with ctl…
4L8D 1.9 Å, Crystal structure of the H2Db in complex with the NP-N5D peptide
3CC5 1.91 Å, H-2Db complex with human gp100
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…

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