7QPJ: MHC class I antigen

Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide. Determined by X-ray diffraction at 1.54 Å resolution. Released 3 Aug 2022.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,098
Mol. weight: 95.29 kDa
Released: 3 Aug 2022

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

Secondary structure: helices and β-sheets

7QPJ contains 32 α-helices and 74 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	8
β-strand	12-15	4	9
α-helix	19	1
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	120-124	5	10
β-strand	126	1	11
β-strand	134-138	5	10
α-helix	146-149	4
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
β-strand	199	1	10

Chain B: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	12
β-strand	11-15	5	13
β-strand	20-22	3	14
β-strand	23-26	4	12
β-strand	32-38	7	13
β-strand	44-52	9	13
β-strand	55-58	4	13
β-strand	65-67	3	14
β-strand	74	1	12
β-strand	77-79	3	14
α-helix	84-86	3
β-strand	88-95	8	13
α-helix	99-100	2
β-strand	101-102	2	13
α-helix	103	1
β-strand	106-111	6	13
α-helix	114-116	3
β-strand	118	1	15
α-helix	119-120	2
β-strand	121-125	5	11
α-helix	126-128	3
α-helix	129-135	7
β-strand	137-147	11	11
β-strand	148	1	15
β-strand	152-158	7	16
β-strand	161-163	3	16
β-strand	167-169	3	11
α-helix	173	1
β-strand	174-175	2	11
β-strand	185-194	10	11
α-helix	195-199	5
β-strand	204-211	8	16
β-strand	214	1	17
α-helix	225-226	2
β-strand	228	1	17
β-strand	230-237	8	16

Chain C: 11 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	51-55	5
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
α-helix	185-186	2
β-strand	187-194	8	3
β-strand	199-209	11	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	242-251	10	3
α-helix	255-257	3
β-strand	258-263	6	4
β-strand	271-273	3	4

Chain D: 3 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
α-helix	47	1
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	C	protein	277	Homo sapiens	A0A140T913 (AlphaFold model)
Beta-2-microglobulin	D	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanoma-associated antigen 10	E	protein	9	Homo sapiens	P43363 (AlphaFold model)
T-cell receptor alpha chain	A	protein	206	Homo sapiens
T-cell receptor beta chain	B	protein	241	Homo sapiens

Sequence of entity 1 (C), FASTA

>7QPJ_1 MHC class I antigen (chains C)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (D), FASTA

>7QPJ_2 Beta-2-microglobulin (chains D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E), FASTA

>7QPJ_3 Melanoma-associated antigen 10 (chains E)
GLYDGMEHL

Sequence of entity 4 (A), FASTA

>7QPJ_4 T-cell receptor alpha chain (chains A)
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSSSFFWYRQYSGKSPELIMSIYANGDKEDG
RFTAQLNKASQYVSLLIRDSQPSDSATYLCAVRGTGRRALTFGSGTRLQVQPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (B), FASTA

>7QPJ_5 T-cell receptor beta chain (chains B)
MNAGVTQTPKFRILKIGQSMTLQCAQDMNHNYMYWYRQDPGMGLKLIYYSVGAGITDKGE
VPNGYNVSRSTTEDFPLRLELAAPSQTSVYFCASSFATEAFFGQGTRLTVVEDLNKVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

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 A0A140T913 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O53 1.4 Å, Structure of HLA-A2:01 with peptide MM96
6O4Z 1.5 Å, Structure of HLA-A2:01 with peptide MM92
6O51 1.55 Å, Structure of HLA-A2:01 with peptide MM90
6O4Y 1.58 Å, Structure of HLA-A2:01 with peptide MM91
7MJ7 1.6 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7P3D 1.67 Å, MHC I A02 Allele presenting YLQPRTFLL
7MJ9 1.75 Å, HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide
7MJ8 1.79 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7SA2 1.85 Å, SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
2P5E 1.89 Å, Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native…
7MKB 1.9 Å, Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL
7U21 1.9 Å, Human Class I MHC HLA-A2 in complex with AVGSYVYSV peptide

Browse structure collections

About this viewer

MolViewer shows 7QPJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.