8EB2: HLA-A*02:01

Structure of HLA-A*02:01 in complex with NY-ESO-1 peptide and PA2.1 Fab. Determined by X-ray diffraction at 2.9 Å resolution. Released 30 Nov 2022.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 15
Atoms: 19,374
Mol. weight: 277.76 kDa
Released: 30 Nov 2022

Explore 8EB2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EB2 contains 91 α-helices and 223 β-strands across 12 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: 11 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	50-54	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	138-149	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	186-193	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
β-strand	228-230	3	3
α-helix	231-233	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

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
α-helix	14-15	2
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	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	78-84	7	7
β-strand	91-94	4	7
α-helix	95-96	2

Chain D: 11 helices, 19 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
β-strand	46-47	2	8
α-helix	50-54	5
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	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-192	7	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
β-strand	228-230	3	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-273	4	11

Chains E and H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
α-helix	14-15	2
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
β-strand	50-51	2	13
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain G: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	15
α-helix	20	1
β-strand	21-28	8	15
β-strand	31-37	7	15
β-strand	46-47	2	15
α-helix	51-54	4
α-helix	57-85	29
β-strand	94-103	10	15
β-strand	109-118	10	15
β-strand	121-126	6	15
β-strand	133-135	3	15
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	16
α-helix	184-185	2
β-strand	186-193	8	17
β-strand	198-208	11	17
β-strand	209	1	16
β-strand	214-219	6	18
β-strand	223	1	18
β-strand	228-230	3	17
α-helix	231-233	3
β-strand	234-235	2	17
β-strand	241-250	10	17
α-helix	254-256	3
β-strand	257-262	6	18
β-strand	270-273	4	18

Chain J: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
α-helix	7-9	3
β-strand	10-12	3	23
β-strand	17-25	9	22
α-helix	29-31	3
β-strand	33-39	7	23
β-strand	45-51	7	23
β-strand	58-60	3	23
β-strand	68-73	6	22
β-strand	78-84	7	22
α-helix	88-90	3
β-strand	92-100	9	23
β-strand	104-108	5	23
β-strand	112-116	5	23
β-strand	122	1	24
α-helix	123-124	2
β-strand	125-129	5	25
β-strand	140-150	11	25
β-strand	151	1	24
β-strand	156-159	4	26
α-helix	160-162	3
β-strand	164	1	26
β-strand	168-170	3	25
α-helix	171-173	3
β-strand	174-175	2	25
β-strand	181-190	10	25
α-helix	192-195	4
β-strand	199-205	7	26
α-helix	206-208	3
β-strand	210-216	7	26

Chain K: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	32
α-helix	7-9	3
β-strand	10-12	3	33
β-strand	18-25	8	32
α-helix	29-31	3
β-strand	34-39	6	33
β-strand	45-52	8	33
β-strand	57-60	4	33
β-strand	68-73	6	32
β-strand	78-83	6	32
α-helix	88-90	3
β-strand	92-100	9	33
β-strand	104-108	5	33
β-strand	112-116	5	33
β-strand	122	1	34
α-helix	123-124	2
β-strand	125-129	5	35
β-strand	140-150	11	35
β-strand	151	1	34
β-strand	156-159	4	36
α-helix	160-162	3
β-strand	168-170	3	35
α-helix	171-173	3
β-strand	174-175	2	35
β-strand	181-190	10	35
α-helix	192-195	4
β-strand	199-205	7	36
β-strand	210-216	7	36

Chain L: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	27
β-strand	10-13	4	28
β-strand	19-25	7	27
β-strand	38-43	6	28
α-helix	48-49	2
β-strand	50-54	5	28
β-strand	58-59	2	28
α-helix	60	1
β-strand	67-72	6	27
β-strand	75-80	6	27
α-helix	85-87	3
β-strand	90-95	6	28
α-helix	101	1
β-strand	102-103	2	28
β-strand	104	1	27
β-strand	107-111	5	28
β-strand	116	1	29
α-helix	117-118	2
β-strand	119-123	5	30
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	30
β-strand	145	1	29
β-strand	149-155	7	31
β-strand	158-159	2	31
α-helix	160	1
β-strand	164-168	5	30
α-helix	169-172	4
β-strand	178-187	10	30
α-helix	188-192	5
β-strand	196-203	8	31
β-strand	210-215	6	31

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA-A*02:01 alpha chain	A, D, G	protein	275	Homo sapiens	A0A140T9X5
Beta-2-microglobulin	B, E, H	protein	100	Homo sapiens	P61769 (AlphaFold model)
NY-ESO-1 peptide	C, F, I	protein	9	Homo sapiens
PA2.1 Fab Heavy Chain	J, K, N	protein	221	Homo sapiens
PA2.1 Fab Light Chain	L, M, O	protein	219	Homo sapiens

Sequence of entity 1 (A, D, G), FASTA

>8EB2_1 HLA-A*02:01 alpha chain (chains A, D, G)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, E, H), FASTA

>8EB2_2 Beta-2-microglobulin (chains B, E, H)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F, I), FASTA

>8EB2_3 NY-ESO-1 peptide (chains C, F, I)
SLLMWITQV

Sequence of entity 4 (J, K, N), FASTA

>8EB2_4 PA2.1 Fab Heavy Chain (chains J, K, N)
QVQLVQSGAEVKKPGSSVKVSCKASGYTFTSYHIHWVRQAPGQGLEWIGWIYPGNVNTEY
NEKFKGKATITADESTNTAYMELSSLRSEDTAVYYCAREEITYAMDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 5 (L, M, O), FASTA

>8EB2_5 PA2.1 Fab Light Chain (chains L, M, O)
DIQMTQSPSTLSASVGDRVTITCRSSQSIVHSNGNTYLEWYQQKPGKAPKLLIYKVSNRF
SGVPARFSGSGSGTEFTLTISSLQPDDFATYYCFQGSHVPRTFGQGTKVEVKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

HLA-A∗02-gated safety switch for cancer therapy has exquisite specificity for its allelic target antigen. Mock, J.Y., Winters, A., Riley, T.P. et al. Mol Ther Oncolytics (2022) 27:157-166. DOI 10.1016/j.omto.2022.09.010 · PubMed

Other PDB entries of the same protein (UniProt A0A140T9X5), best resolution first:

7TR4 2.3 Å, MA2-MART1-HLAA0201

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