6TRO: T-cell receptor GVY01

Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV. Determined by X-ray diffraction at 3.0 Å resolution. Released 24 Jun 2020.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,595
Mol. weight: 96.38 kDa
Released: 24 Jun 2020

Explore 6TRO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TRO contains 22 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	19-20	2
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	122-126	5	1
β-strand	133-135	3	1
α-helix	138-149	12
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
α-helix	184-185	2
β-strand	186-194	9	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	223-224	2	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-249	9	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	45	1	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: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	36-44	9	9
β-strand	51-56	6	9
β-strand	65-68	4	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	117-118	2	9
β-strand	122-127	6	9
β-strand	136-140	5	10
β-strand	142	1	11
β-strand	150-154	5	10
β-strand	171-172	2	10
α-helix	173-175	3
β-strand	176-180	5	10
β-strand	185-193	9	10
β-strand	215	1	10

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	12
β-strand	10-14	5	13
β-strand	19-24	6	12
β-strand	39-45	7	13
β-strand	49-56	8	13
β-strand	67-68	2	13
β-strand	76-79	4	12
β-strand	86-91	6	12
α-helix	96-98	3
β-strand	100-106	7	13
β-strand	117-118	2	13
β-strand	122-127	6	13
α-helix	130-132	3
β-strand	134	1	14
α-helix	135-136	2
β-strand	137-141	5	11
α-helix	142-144	3
α-helix	145-151	7
β-strand	153-163	11	11
β-strand	164	1	14
β-strand	168-174	7	15
β-strand	178-179	2	15
β-strand	183-185	3	11
α-helix	189	1
β-strand	190-191	2	11
β-strand	201-210	10	11
α-helix	211-215	5
β-strand	220-227	8	15
β-strand	230	1	16
α-helix	241-242	2
β-strand	244	1	16
β-strand	246-253	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	Q53Z42 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
MAGE-A4 peptide (amino acids 230-239)	C	protein	10	Homo sapiens	P43358 (AlphaFold model)
T-cell receptor alpha chain	D	protein	208	Homo sapiens
T-cell receptor beta chain	E	protein	247	Homo sapiens

Sequence of entity 1 (A), FASTA

>6TRO_1 MHC class I antigen (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>6TRO_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6TRO_3 MAGE-A4 peptide (amino acids 230-239) (chains C)
GVYDGREHTV

Sequence of entity 4 (D), FASTA

>6TRO_4 T-cell receptor alpha chain (chains D)
MKNQVEQSPQSLIILEGKNVTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSN
GRYTATLDADTKQSSLHITASQLSDSASYICVVNHSGGSYIPTFGRGTSLIVHPYIQKPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6TRO_5 T-cell receptor beta chain (chains E)
MDVKVTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGD
IPEGYSVSREKKERFSLILESASTNQTSMYLCASSFLMTSGDPYEQYFGPGTRLTVTEDL
KNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRAD

Primary citation

T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4. Coles, C.H., McMurran, C., Lloyd, A. et al. J Biol Chem (2020) 295:11486-11494. DOI 10.1074/jbc.RA120.014016 · 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
7RTR 2.6 Å, YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL)…
8TBV 2.64 Å, Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL
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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