6P64: MHC class I antigen

Alpha-beta TCR Binding to Neoantigen KQWLVWLFL Presented by HLA-A206. Determined by X-ray diffraction at 3.05 Å resolution. Released 3 Jun 2020.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,284
Mol. weight: 193.34 kDa
Released: 3 Jun 2020

Explore 6P64 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P64 contains 47 α-helices and 143 β-strands across 8 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	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-53	4
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
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-192	7	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	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	270-273	4	4

Chains B and G: 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
α-helix	46	1
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 D: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	15
β-strand	11-15	5	16
β-strand	20-22	3	15
β-strand	25-26	2	15
β-strand	34-40	7	16
β-strand	47-53	7	16
β-strand	65-70	6	15
β-strand	75-80	6	15
α-helix	85-87	3
β-strand	89-96	8	16
β-strand	103-104	2	16
β-strand	108-113	6	16
β-strand	122-128	7	17
β-strand	135-140	6	17
β-strand	157-158	2	17
α-helix	159-161	3
β-strand	162-166	5	17
β-strand	171-179	9	17
α-helix	187-189	3
β-strand	201	1	17

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	18
β-strand	11-15	5	19
β-strand	20-25	6	18
β-strand	32-38	7	19
β-strand	44-51	8	19
β-strand	54-57	4	19
β-strand	66-72	7	18
β-strand	75-80	6	18
α-helix	85-87	3
β-strand	89-96	8	19
α-helix	103-104	2
β-strand	105-106	2	19
β-strand	110-115	6	19
α-helix	118-120	3
β-strand	122	1	20
α-helix	123-124	2
β-strand	125-130	6	17
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	17
β-strand	152	1	20
β-strand	156-162	7	21
β-strand	165-167	3	21
β-strand	171-173	3	17
β-strand	178-179	2	17
β-strand	189-198	10	17
α-helix	199-202	4
β-strand	208-215	8	21
β-strand	218	1	22
β-strand	232	1	22
β-strand	234-241	8	21
α-helix	242-243	2

Chain F: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
α-helix	45	1
β-strand	46-47	2	8
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-189	4	10
β-strand	203-208	6	10
β-strand	209	1	9
β-strand	214-216	3	11
β-strand	230	1	10
β-strand	234-235	2	10
β-strand	241-245	5	10
β-strand	258-262	5	11
β-strand	270-273	4	11

Chain I: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	23
β-strand	11-15	5	24
β-strand	20-22	3	23
β-strand	25-27	3	23
β-strand	34-40	7	24
β-strand	47-53	7	24
β-strand	65-70	6	23
β-strand	75-80	6	23
α-helix	85-87	3
β-strand	89-96	8	24
β-strand	103-104	2	24
β-strand	108-113	6	24
β-strand	122-126	5	25
β-strand	127	1	26
α-helix	128-129	2
β-strand	135-140	6	25
β-strand	156-158	3	25
α-helix	159-161	3
β-strand	162-166	5	25
β-strand	171-180	10	25
α-helix	187-189	3
β-strand	201	1	25

Chain J: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	27
β-strand	11-15	5	28
β-strand	20-25	6	27
α-helix	26	1
β-strand	32-38	7	28
β-strand	44-51	8	28
β-strand	54-57	4	28
β-strand	66-72	7	27
β-strand	75-80	6	27
α-helix	85-87	3
β-strand	89-96	8	28
α-helix	103-104	2
β-strand	105-106	2	28
β-strand	110-115	6	28
α-helix	118-120	3
β-strand	122	1	29
α-helix	123-124	2
β-strand	125-129	5	30
β-strand	130	1	26
α-helix	131-132	2
α-helix	133-138	6
β-strand	141-151	11	30
β-strand	152	1	29
β-strand	156-162	7	31
β-strand	165-167	3	31
β-strand	171-173	3	30
β-strand	178-179	2	30
β-strand	189-198	10	30
α-helix	199-202	4
β-strand	208-215	8	31
β-strand	218	1	32
β-strand	232	1	32
β-strand	234-241	8	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, F	protein	276	Homo sapiens	Q53Z42 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
302TIL TCR alpha chain	D, I	protein	208	Homo sapiens
302TIL TCR beta chain	E, J	protein	245	Homo sapiens
Neoantigen peptide KQWLVWLFL	C, H	protein	9	Homo sapiens	Q5VTY9 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>6P64_1 MHC class I antigen (chains A, F)
MGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, G), FASTA

>6P64_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D, I), FASTA

>6P64_3 302TIL TCR alpha chain (chains D, I)
MAQTVTQSQPEMSVQEAETVTLSCTYDTSESDYYLFWYKQPPSRQMILVIRQEAYKQQNA
TENRFSVNFQKAAKSFSLKISDSQLGDAAMYFCAFMDSNYQLIWGAGTKLIIKPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E, J), FASTA

>6P64_4 302TIL TCR beta chain (chains E, J)
MDAGVIQSPRHEVTEMGQEVTLRCKPISGHNSLFWYRQTMMRGLELLIYFNNNVPIDDSG
MPEDRFSAKMPNASFSTLKIQPSEPRDSAVYFCASSRTSPTDTQYFGPGTRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Sequence of entity 5 (C, H), FASTA

>6P64_5 Neoantigen peptide KQWLVWLFL (chains C, H)
KQWLVWLFL

Primary citation

A T cell receptor peptide/MHC complex at 3.05 Angstrom resolution. Devlin, J.R., Baker, B.M., Harari, A. To be published.

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
6TRO 3.0 Å, Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV

Browse structure collections

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