7N5C: 6218 TCR

6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond. Determined by X-ray diffraction at 1.87 Å resolution. Released 20 Jul 2022.

Method: X-ray diffraction
Resolution: 1.87 Å
Organisms: Mus musculus, Homo sapiens, Influenza A virus
Chains: 5
Atoms: 6,898
Mol. weight: 95.32 kDa
Released: 20 Jul 2022

Explore 7N5C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N5C contains 24 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	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
α-helix	87-88	2
β-strand	93-103	11	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	152-161	10
α-helix	163-174	12
α-helix	176-180	5
β-strand	183	1	2
α-helix	184-185	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	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

Chain B: 2 helices, 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
α-helix	52-54	3
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 D: 7 helices, 19 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	37-44	8	9
β-strand	51-56	6	9
β-strand	66-67	2	8
β-strand	77-80	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	134-137	4	10
α-helix	138	1
β-strand	139	1	11
α-helix	140-141	2
β-strand	149-152	4	10
β-strand	159	1	12
α-helix	161-163	3
β-strand	169-170	2	10
α-helix	171-173	3
β-strand	174-178	5	10
α-helix	179-181	3
β-strand	183-191	9	10
α-helix	199-202	4
β-strand	207	1	12
β-strand	213	1	10

Chain E: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	13
β-strand	10-14	5	14
β-strand	19-21	3	15
β-strand	24-25	2	13
β-strand	38-44	7	14
β-strand	51-58	8	14
β-strand	65-68	4	14
β-strand	77-79	3	15
β-strand	86	1	13
β-strand	88-91	4	15
α-helix	96-98	3
β-strand	100-107	8	14
β-strand	113-114	2	14
β-strand	118-123	6	14
β-strand	130	1	16
α-helix	131-132	2
β-strand	133-137	5	17
β-strand	138	1	11
α-helix	139-140	2
α-helix	141-147	7
β-strand	149-159	11	17
β-strand	160	1	16
β-strand	164-170	7	18
β-strand	173-175	3	18
β-strand	179-181	3	17
α-helix	185	1
β-strand	186-187	2	17
β-strand	197-206	10	17
α-helix	207-211	5
β-strand	216-223	8	18
β-strand	226	1	19
β-strand	240	1	19
β-strand	242-249	8	18

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 with 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

>7N5C_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPS

Sequence of entity 2 (B), FASTA

>7N5C_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7N5C_3 peptide from Polymerase acidic protein (chains C)
SSLCNFRAYV

Sequence of entity 4 (D), FASTA

>7N5C_4 Fusion protein of T cell receptor alpha variable 21-DV12 with T-cell receptor, sp3.4 alpha chain (chains D)
DAKTTQPDSMESTEGETVHLPCSHATISGNEYIYWYRQVPLQGPEYVTHGLQQNTTNSMA
FLAIASDRKSSTLILPHVSLRDAAVYHCILSGGCNYKLTFGKGTLLTVTPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>7N5C_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
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…
5M01 1.95 Å, Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from…

Browse structure collections

About this viewer

MolViewer shows 7N5C directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.