5BRZ: MAGE-A3 reactive TCR

MAGE-A3 reactive TCR in complex with MAGE-A3 in HLA-A1. Determined by X-ray diffraction at 2.62 Å resolution. Released 2 Mar 2016.

Method: X-ray diffraction
Resolution: 2.62 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,618
Mol. weight: 93.91 kDa
Released: 2 Mar 2016

Explore 5BRZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5BRZ contains 21 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 A: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	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	152-161	10
α-helix	163-174	12
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	213-219	7	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
β-strand	257-263	7	4
β-strand	270-272	3	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
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
α-helix	95-96	2

Chain D: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	8
β-strand	11-15	5	9
β-strand	20-26	7	8
β-strand	31-39	9	9
β-strand	45-51	7	9
β-strand	57-60	4	8
β-strand	63-68	6	8
β-strand	73-78	6	8
β-strand	87-95	9	9
β-strand	104-105	2	9
β-strand	109-114	6	9
β-strand	123-129	7	10
β-strand	136-141	6	10
α-helix	151-153	3
β-strand	158-159	2	10
α-helix	160-162	3
β-strand	165-166	2	11
β-strand	173-174	2	11
β-strand	176-180	5	10
α-helix	188-191	4

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	12
β-strand	11-15	5	13
β-strand	20-25	6	12
α-helix	26-27	2
β-strand	32-39	8	13
β-strand	43-51	9	13
β-strand	54-58	5	13
β-strand	65-69	5	12
β-strand	75-79	5	12
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	102-104	3	13
β-strand	108-113	6	13
α-helix	116-118	3
β-strand	120	1	14
β-strand	123-128	6	10
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	10
β-strand	150	1	14
β-strand	154-160	7	15
β-strand	163-165	3	15
β-strand	169-171	3	10
β-strand	176-177	2	10
β-strand	187-196	10	10
α-helix	197-200	4
β-strand	206-213	8	15
β-strand	216	1	16
α-helix	227-228	2
β-strand	230	1	16
β-strand	232-239	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-1 alpha chain	A	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Glu-val-asp-pro-ile-gly-his-leu-tyr	C	protein	9	Homo sapiens	P43357 (AlphaFold model)
Protein TRAV21,T-cell receptor alpha chain C region	D	protein	197	Homo sapiens	A0A0B4J279 (AlphaFold model), P01848
Protein TRBV5-1,Human nkt tcr beta chain	E	protein	241	Homo sapiens	A0A578, A0A5B9

Sequence of entity 1 (A), FASTA

>5BRZ_1 HLA class I histocompatibility antigen, A-1 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYW
DQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG
KDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWP

Sequence of entity 2 (B), FASTA

>5BRZ_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>5BRZ_3 GLU-VAL-ASP-PRO-ILE-GLY-HIS-LEU-TYR (chains C)
EVDPIGHLY

Sequence of entity 4 (D), FASTA

>5BRZ_4 Protein TRAV21,T-cell receptor alpha chain C region (chains D)
AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLYVRPYQREQTSG
RLNASLDKSSGRSTLYIAASQPGDSATYLCAVRPGGAGPFFVVFGKGTKLSVIPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIP

Sequence of entity 5 (E), FASTA

>5BRZ_5 Protein TRBV5-1,Human nkt tcr beta chain (chains E)
AGVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFP
GRFSGRQFSNSRSEMNVSTLELGDSALYLCASSFNMATGQYFGPGTRLTVTEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Primary citation

Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy. Raman, M.C., Rizkallah, P.J., Simmons, R. et al. Sci Rep (2016) 6:18851-18851. DOI 10.1038/srep18851 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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