7RTR: YLQ-SG3 TCR

YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01. Determined by X-ray diffraction at 2.6 Å resolution. Released 13 Oct 2021.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 5
Atoms: 6,644
Mol. weight: 104.38 kDa
Released: 13 Oct 2021

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

Secondary structure: helices and β-sheets

7RTR contains 26 α-helices and 72 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
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	140-149	10
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-192	7	3
β-strand	200-208	9	3
β-strand	209	1	2
β-strand	213-217	5	4
β-strand	224	1	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-247	7	3
β-strand	259-263	5	4
β-strand	270-272	3	4

Chain B: 4 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
α-helix	46	1
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
α-helix	95-96	2

Chain D: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	8
β-strand	11-14	4	9
α-helix	18	1
β-strand	19-25	7	8
β-strand	39-44	6	9
β-strand	51-56	6	9
β-strand	64-68	5	8
β-strand	76-81	6	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-108	9	9
β-strand	111-114	4	9
β-strand	118-123	6	9
β-strand	132-137	6	10
β-strand	138	1	11
β-strand	145-150	6	10
β-strand	166-168	3	10
α-helix	169-171	3
β-strand	172-176	5	10
α-helix	177-179	3
β-strand	181-190	10	10
α-helix	197-199	3
β-strand	211	1	10

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
β-strand	38-44	7	13
α-helix	49-50	2
β-strand	51-57	7	13
β-strand	64-68	5	13
β-strand	76-79	4	12
β-strand	87-91	5	12
α-helix	96-98	3
β-strand	100-107	8	13
β-strand	113-114	2	13
β-strand	118-123	6	13
α-helix	126-128	3
β-strand	130	1	14
α-helix	131-132	2
β-strand	133-137	5	11
α-helix	138-140	3
α-helix	141-147	7
β-strand	149-159	11	11
β-strand	160	1	14
β-strand	164-170	7	15
β-strand	173-175	3	15
β-strand	179-181	3	11
α-helix	185	1
β-strand	186-187	2	11
β-strand	197-206	10	11
α-helix	207-210	4
β-strand	216-223	8	15
β-strand	226	1	16
α-helix	237-238	2
β-strand	240	1	16
β-strand	242-249	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I antigen	A	protein	365	Homo sapiens	Q53Z42 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Spike protein S1	C	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
YLQ-SG3 TCR alpha chain (TRAV12-2)	D	protein	203	Homo sapiens
YLQ-SG3 TCR beta chain (TRBV7-9)	E	protein	241	Homo sapiens

Sequence of entity 1 (A), FASTA

>7RTR_1 HLA class I antigen (chains A)
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQ
RMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQL
RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP
SSQPTIPIVGIIAGLVLFGAVITGAVVAAVMWRRKSSDRKGGSYSQAASSDSAQGSDVSL
TACKV

Sequence of entity 2 (B), FASTA

>7RTR_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7RTR_3 Spike protein S1 (chains C)
YLQPRTFLL

Sequence of entity 4 (D), FASTA

>7RTR_4 YLQ-SG3 TCR alpha chain (TRAV12-2) (chains D)
QKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGR
FTAQLNKASQYVSLLIRDSQPSDSATYLCAVNRDDKIIFGKGTRLHILPNIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>7RTR_5 YLQ-SG3 TCR beta chain (TRBV7-9) (chains E)
DTGVSQNPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSRL
LSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSPDIEQYFGPGTRLTVTEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Primary citation

Molecular Basis of a Dominant SARS-CoV-2 Spike-Derived Epitope Presented by HLA-A*02:01 Recognised by a Public TCR. Szeto, C., Nguyen, A.T., Lobos, C.A. et al. Cells (2021) 10. DOI 10.3390/cells10102646 · PubMed

Other PDB entries of the same protein (UniProt Q53Z42 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TRN 1.35 Å, Crystal structure of HLA A2*01-AVYDGREHTV
8FU4 1.6 Å, HCMV US11 peptide binding to HLA-A*02:01
7UM2 1.63 Å, SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by…
7U1R 1.8 Å, SARS-CoV-2 Spike-derived peptide S1185-1193 K1191N mutant (RLNEVANNL) presented by…
8RBV 1.8 Å, SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by…
22EE 1.99 Å, Structure of HLA-A2:01 with 9-mer peptide PGS
7RTD 2.05 Å, SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01
9MIN 2.05 Å, Structure of a designed minibinder to NYESO1-A*02:01
7UR1 2.17 Å, SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01
8TBV 2.64 Å, Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL
6TRO 3.0 Å, Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV
9VSO 3.03 Å, Crystal structure of Fab bound to the WT1-derived RMF peptide presented by HLA-A*02:01

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