7PBC: MHC class I antigen

Crystal structure of engineered TCR (796) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide. Determined by X-ray diffraction at 2.04 Å resolution. Released 3 Aug 2022.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,826
Mol. weight: 95.3 kDa
Released: 3 Aug 2022

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

Secondary structure: helices and β-sheets

7PBC contains 28 α-helices and 71 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 AAA: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	8
β-strand	12-15	4	9
β-strand	20-26	7	8
β-strand	33-39	7	9
β-strand	46-51	6	9
β-strand	55-59	5	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-93	8	9
α-helix	100	1
β-strand	101-102	2	9
α-helix	103	1
β-strand	106-111	6	9
β-strand	120-126	7	10
β-strand	133-138	6	10
α-helix	147-149	3
β-strand	154-156	3	10
α-helix	157-159	3
β-strand	160-164	5	10
α-helix	165-167	3
β-strand	169-178	10	10
α-helix	185-188	4
α-helix	194-195	2
β-strand	199	1	10

Chain BBB: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-8	4	11
β-strand	11-15	5	12
β-strand	20-26	7	11
β-strand	32-39	8	12
β-strand	43-52	10	12
β-strand	55-58	4	12
β-strand	65-68	4	11
β-strand	74-79	6	11
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	101-102	2	12
β-strand	106-111	6	12
α-helix	114-116	3
β-strand	118	1	13
α-helix	119-120	2
β-strand	121-126	6	10
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	10
β-strand	148	1	13
β-strand	152-158	7	14
β-strand	161-163	3	14
β-strand	167-169	3	10
α-helix	173	1
β-strand	174-175	2	10
β-strand	185-194	10	10
α-helix	195-199	5
β-strand	204-211	8	14
β-strand	214	1	15
α-helix	225-226	2
β-strand	228	1	15
β-strand	230-237	8	14

Chain CCC: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
α-helix	21	1
β-strand	22-29	8	1
β-strand	32-38	7	1
β-strand	47-48	2	1
α-helix	52-55	4
α-helix	58-86	29
β-strand	95-104	10	1
β-strand	110-119	10	1
β-strand	122-127	6	1
β-strand	134-136	3	1
α-helix	139-150	12
α-helix	153-159	7
α-helix	160-164	5
α-helix	165-175	11
α-helix	177-180	4
β-strand	184	1	2
β-strand	187-194	8	3
β-strand	200-209	10	3
β-strand	210	1	2
β-strand	215-220	6	4
β-strand	223-224	2	4
β-strand	230-231	2	3
α-helix	232-234	3
β-strand	235-236	2	3
β-strand	242-250	9	3
β-strand	258-263	6	4
β-strand	271-273	3	4

Chain DDD: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	CCC	protein	277	Homo sapiens	Q861F7 (AlphaFold model)
Beta-2-microglobulin	DDD	protein	100	Homo sapiens	P61769 (AlphaFold model)
T-cell receptor (TRAV/TRAC)	AAA	protein	206	Homo sapiens
T-cell receptor (TRBV/TRBC)	BBB	protein	241	Homo sapiens
Melanoma-associated antigen 10	EEE	protein	9	Homo sapiens	P43363 (AlphaFold model)

Sequence of entity 1 (CCC), FASTA

>7PBC_1 MHC class I antigen (chains CCC)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (DDD), FASTA

>7PBC_2 Beta-2-microglobulin (chains DDD)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (AAA), FASTA

>7PBC_3 T-cell receptor (TRAV/TRAC) (chains AAA)
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKEDG
RFTAQLNKASQYVSLLIRDSQPSDSATYLCAVRGTGRRALTFGSGTRLQVQPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (BBB), FASTA

>7PBC_4 T-cell receptor (TRBV/TRBC) (chains BBB)
MNAGVTQTPKFRVLKTGQSMTLLCAQDMNHDYMYWYRQDPGMGLRLIHYSVGEGTTAKGE
VPDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASSFTDTQYFGPGTRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Sequence of entity 5 (EEE), FASTA

>7PBC_5 Melanoma-associated antigen 10 (chains EEE)
GLYDGMEHL

Primary citation

Structural insights into engineering a T-cell receptor targeting MAGE-A10 with higher affinity and specificity for cancer immunotherapy. Simister, P.C., Border, E.C., Vieira, J.F. et al. J Immunother Cancer (2022) 10. DOI 10.1136/jitc-2022-004600 · PubMed

Other PDB entries of the same protein (UniProt Q861F7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KGQ 1.34 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N222-230
7KGP 1.4 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N316-324
7KGR 1.55 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N159-167
7KGS 1.58 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N138-146
7T5M 1.67 Å, Structure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex
7PDW 1.82 Å, Crystal structure of parent TCR (728) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer…
7KGT 1.9 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234
7SIS 1.9 Å, SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01
7KGO 2.15 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N351-359
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
8FJA 3.0 Å, CryoEM structure of HLA-A2 MAGEA4 (230-239) in complex with REGN6972 Fab
8FJB 3.06 Å, CryoEM structure of HLA-A2 MAGEA4 (286-294) in complex with H2aM31345N Fab

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