7PDW: T-cell receptor alpha chain

Crystal structure of parent TCR (728) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide. Determined by X-ray diffraction at 1.82 Å resolution. Released 3 Aug 2022.

Method: X-ray diffraction
Resolution: 1.82 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,742
Mol. weight: 190.28 kDa
Ligands: PO4
Released: 3 Aug 2022

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

Secondary structure: helices and β-sheets

7PDW contains 57 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 AAA: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	12-15	4	2
α-helix	19	1
β-strand	20-26	7	1
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	55-59	5	1
β-strand	62-67	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-93	8	2
α-helix	100	1
β-strand	101-102	2	2
α-helix	103	1
β-strand	106-111	6	2
β-strand	120-125	6	3
β-strand	126	1	4
β-strand	133-138	6	3
α-helix	146-149	4
β-strand	154-156	3	3
α-helix	157-159	3
β-strand	160-164	5	3
β-strand	169-178	10	3
α-helix	185-188	4
β-strand	199	1	3

Chain BBB: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	5
β-strand	11-15	5	6
β-strand	20-26	7	5
β-strand	32-39	8	6
β-strand	43-52	10	6
β-strand	55-58	4	6
β-strand	66-68	3	5
β-strand	74-79	6	5
α-helix	84-86	3
β-strand	88-95	8	6
β-strand	101-102	2	6
β-strand	106-111	6	6
α-helix	114-116	3
β-strand	118	1	7
α-helix	119-120	2
β-strand	121-125	5	4
α-helix	126-128	3
α-helix	129-135	7
β-strand	137-147	11	4
β-strand	148	1	7
β-strand	152-158	7	8
β-strand	161-163	3	8
β-strand	167-169	3	4
α-helix	173	1
β-strand	174-175	2	4
β-strand	185-194	10	4
α-helix	195-199	5
β-strand	204-211	8	8
β-strand	214	1	9
α-helix	225-226	2
β-strand	228	1	9
β-strand	230-237	8	8

Chain CCC: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	24
α-helix	21	1
β-strand	22-29	8	24
β-strand	32-38	7	24
β-strand	47-48	2	24
α-helix	51-55	5
α-helix	58-85	28
β-strand	95-104	10	24
β-strand	110-119	10	24
β-strand	122-127	6	24
β-strand	134-136	3	24
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	25
α-helix	185-186	2
β-strand	187-194	8	26
β-strand	199-209	11	26
β-strand	210	1	25
β-strand	215-220	6	27
β-strand	223-224	2	27
α-helix	226-228	3
β-strand	229-231	3	26
α-helix	232-234	3
β-strand	235-236	2	26
β-strand	242-251	10	26
α-helix	255-257	3
β-strand	258-263	6	27
β-strand	271-273	3	27

Chains DDD and III: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	10
α-helix	5-6	2
β-strand	7-12	6	11
β-strand	22-31	10	11
β-strand	32	1	10
β-strand	37-42	6	12
β-strand	45-46	2	12
β-strand	51-52	2	11
α-helix	53-55	3
β-strand	56-57	2	11
β-strand	63-71	9	11
β-strand	79-84	6	12
β-strand	92-95	4	12

Chain FFF: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	13
β-strand	12-15	4	14
α-helix	19	1
β-strand	20-26	7	13
β-strand	33-39	7	14
β-strand	46-51	6	14
β-strand	55-59	5	13
β-strand	62-67	6	13
β-strand	72-77	6	13
α-helix	82-84	3
β-strand	86-93	8	14
α-helix	100	1
β-strand	101-102	2	14
α-helix	103	1
β-strand	106-111	6	14
β-strand	120-126	7	15
β-strand	133-138	6	15
α-helix	146-149	4
β-strand	154-156	3	15
α-helix	157-159	3
β-strand	160-164	5	15
β-strand	169-178	10	15
α-helix	185-188	4
β-strand	199	1	15

Chain GGG: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	16
β-strand	11-15	5	17
β-strand	20-26	7	16
β-strand	32-39	8	17
β-strand	43-52	10	17
β-strand	55-58	4	17
β-strand	66-68	3	16
β-strand	74-79	6	16
α-helix	84-86	3
β-strand	88-95	8	17
β-strand	101-102	2	17
β-strand	106-111	6	17
α-helix	114-116	3
β-strand	118	1	18
α-helix	119-120	2
β-strand	121-126	6	15
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	15
β-strand	148	1	18
β-strand	152-158	7	19
β-strand	161-163	3	19
β-strand	167-169	3	15
α-helix	173	1
β-strand	174-175	2	15
β-strand	185-194	10	15
α-helix	195-199	5
β-strand	204-211	8	19
β-strand	214	1	20
α-helix	225-226	2
β-strand	228	1	20
β-strand	230-237	8	19

Chain HHH: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	28
α-helix	21	1
β-strand	22-29	8	28
β-strand	32-38	7	28
β-strand	47-48	2	28
α-helix	51-55	5
α-helix	58-85	28
β-strand	95-104	10	28
β-strand	110-119	10	28
β-strand	122-127	6	28
β-strand	134-136	3	28
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	29
α-helix	185-186	2
β-strand	187-194	8	30
β-strand	199-209	11	30
β-strand	210	1	29
β-strand	215-220	6	31
β-strand	223-225	3	31
β-strand	229-231	3	30
α-helix	232-234	3
β-strand	235-236	2	30
β-strand	242-251	10	30
α-helix	255-257	3
β-strand	258-263	6	31
β-strand	271-274	4	31

Molecules and chains

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

Sequence of entity 1 (AAA, FFF), FASTA

>7PDW_1 T-cell receptor alpha chain (TRAV/TRAC) (chains AAA, FFF)
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKEDG
RFTAQLNKASQYVSLLIRDSQPSDSATYLCAVRGTGRRALTFGSGTRLQVQPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (BBB, GGG), FASTA

>7PDW_2 T-cell receptor beta chain (TRBV/TRBC) (chains BBB, GGG)
MNAGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGE
VPDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASSFTDTQYFGPGTRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Sequence of entity 3 (DDD, III), FASTA

>7PDW_3 Beta-2-microglobulin (chains DDD, III)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 4 (EEE, JJJ), FASTA

>7PDW_4 Melanoma-associated antigen 10 (chains EEE, JJJ)
GLYDGMEHL

Sequence of entity 5 (CCC, HHH), FASTA

>7PDW_5 MHC class I antigen (chains CCC, HHH)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (GOL) are not listed.

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 P61769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4E0K 0.97 Å, Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2…
1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
2YXF 1.13 Å, The high resolution crystal structure of beta2-microglobulin under physiological…
8E2Z 1.13 Å, Structures of HLA-B8E76C loaded with long peptides reveal novel features at the…
7NMR 1.15 Å, Crystal structure of beta-2-microglobulin D76S mutant
8ROP 1.15 Å, Crystal structure of HLA B*18:01 in complex with QEIRTFSF, an 8-mer epitope from…
7R7W 1.17 Å, Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9 S3T variant
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6Y26 1.2 Å, Crystal structure of HLA-B2705 complexed with the nona-peptide mA
7NMC 1.2 Å, Crystal structure of beta-2-microglobulin D76E mutant

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