6TMO: MHC class I antigen

Structure determination of an enhanced affinity TCR, a24b17, in complex with HLA-A*02:01 presenting a MART-1 peptide, EAAGIGILTV. Determined by X-ray diffraction at 2.1 Å resolution. Released 7 Oct 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,167
Mol. weight: 95.92 kDa
Ligands: TAM
Released: 7 Oct 2020

Explore 6TMO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TMO contains 26 α-helices and 72 β-strands across 5 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, 18 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	186-194	9	3
β-strand	196-208	13	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	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
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	8

Chain D: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	11-14	4	10
α-helix	18	1
β-strand	19-25	7	9
β-strand	32-38	7	10
β-strand	45-50	6	10
β-strand	54-58	5	9
β-strand	61-66	6	9
β-strand	71-76	6	9
α-helix	81-83	3
β-strand	85-92	8	10
β-strand	97-99	3	10
β-strand	103-108	6	10
β-strand	117-121	5	11
β-strand	130-135	6	11
β-strand	152-153	2	11
α-helix	154-156	3
β-strand	157-161	5	11
α-helix	163-165	3
β-strand	166-175	10	11
α-helix	182-185	4
β-strand	194	1	11

Chain E: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-14	5	13
β-strand	19-26	8	12
β-strand	32-38	7	13
β-strand	45-51	7	13
β-strand	54-58	5	13
β-strand	65-70	6	12
β-strand	73-78	6	12
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	98	1	8
β-strand	102-105	4	13
β-strand	109-114	6	13
α-helix	117-119	3
β-strand	121	1	14
α-helix	122-123	2
β-strand	124-128	5	15
α-helix	129-131	3
α-helix	132-137	6
β-strand	140-150	11	15
β-strand	151	1	14
β-strand	155-161	7	16
β-strand	164-166	3	16
β-strand	170-172	3	15
β-strand	177-178	2	15
β-strand	188-197	10	15
α-helix	198-202	5
β-strand	207-214	8	16
β-strand	217	1	17
α-helix	228-229	2
β-strand	231	1	17
β-strand	233-240	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	A0A5B8RNS7 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Eaagigiltv	C	protein	10	Homo sapiens	Q16655 (AlphaFold model)
Alpha chain of engineered high affinity T-cell receptor	D	protein	197	Homo sapiens
Beta chain of high affinity engineered T-cell receptor	E	protein	244	Homo sapiens

Sequence of entity 1 (A), FASTA

>6TMO_1 MHC class I antigen (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>6TMO_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6TMO_3 EAAGIGILTV (chains C)
EAAGIGILTV

Sequence of entity 4 (D), FASTA

>6TMO_4 Alpha chain of engineered high affinity T-cell receptor (chains D)
KQEVEQNSGPLSVPEGAIASLNCTYSFLGSQSFFWYRQYSGKSPELIMFTYREGDKEDGR
FTAQLNKASQHVSLLIRDSQPSDSATYLCAVNDGGRLTFGDGTTLTVKPNIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFF

Sequence of entity 5 (E), FASTA

>6TMO_5 Beta chain of high affinity engineered T-cell receptor (chains E)
SQTIHQWPATLVQPVGSPLSLECTVEGTSNPNLYWYRQAAGRGPQLLFYWGPFGQISSEV
PQNLSASRPQDRQFILSSKKLLLSDSGFYLCAWSETGLGMGGWQFGEGSRLTVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Ligands and cofactors

ID	Name	Formula	Copies
TAM	Tris(hydroxyethyl)aminomethane	C7 H17 N O3	3

Water and common crystallization additives (GOL, EDO, SO4) are not listed.

Primary citation

Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy. Crean, R.M., MacLachlan, B.J., Madura, F. et al. Mol Ther Oncolytics (2020) 18:443-456. DOI 10.1016/j.omto.2020.07.008 · PubMed

Other PDB entries of the same protein (UniProt A0A5B8RNS7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GV7 1.86 Å, Structure of reverse docking TCR in complex with peptide-HLA
9DL1 2.3 Å, Crystal Structure of HLA-A*02:01/NY-ESO-1 (SLLMWITQV) and a target specific TRACeR-I
9SOK 2.5 Å, Structure of three-domain single chain TCR-581 in complex with Peptide-HLA
9GV6 2.77 Å, Structure of TCR in complex with peptide-HLA
9SOL 2.93 Å, Structure of TCR-581 in complex with Peptide-HLA

Browse structure collections

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