6PUM: Human MAIT A-F7 TCR

Structure of human MAIT A-F7 TCR in complex with human MR1-2'D-5-OP-RU. Determined by X-ray diffraction at 1.96 Å resolution. Released 19 Feb 2020.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,699
Mol. weight: 189.37 kDa
Ligands: Q84
Released: 19 Feb 2020

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

Secondary structure: helices and β-sheets

6PUM contains 55 α-helices and 147 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 A: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	15-16	2
β-strand	22-28	7	1
β-strand	31-37	7	1
β-strand	44-45	2	1
α-helix	48-51	4
α-helix	56-84	29
β-strand	91-100	10	1
β-strand	106-114	9	1
β-strand	117-123	7	1
β-strand	128-131	4	1
α-helix	134-144	11
α-helix	147-155	9
α-helix	156-160	5
α-helix	161-171	11
α-helix	173-176	4
β-strand	180	1	2
α-helix	181-182	2
β-strand	183-188	6	3
β-strand	197-205	9	3
β-strand	206	1	2
β-strand	211-216	6	4
β-strand	219-220	2	4
α-helix	225	1
β-strand	226-227	2	3
α-helix	228-230	3
β-strand	231-232	2	3
β-strand	238-245	8	3
β-strand	254-260	7	4
β-strand	263-268	6	4

Chain B: 2 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
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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	15-16	2
β-strand	22-28	7	8
β-strand	31-37	7	8
β-strand	44-45	2	8
α-helix	48-51	4
α-helix	56-84	29
β-strand	91-100	10	8
β-strand	106-114	9	8
β-strand	117-123	7	8
β-strand	128-131	4	8
α-helix	134-144	11
α-helix	147-155	9
α-helix	156-160	5
α-helix	161-171	11
α-helix	173-176	4
β-strand	180	1	9
α-helix	181-182	2
β-strand	183-190	8	10
β-strand	196-205	10	10
β-strand	206	1	9
β-strand	211-216	6	11
β-strand	219-220	2	11
α-helix	224-225	2
β-strand	226-227	2	10
β-strand	231-232	2	10
β-strand	238-246	9	10
α-helix	247	1
β-strand	254-260	7	11
β-strand	263-268	6	11

Chain D: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	12
β-strand	9-13	5	13
β-strand	18-25	8	12
β-strand	32-37	6	13
β-strand	44-49	6	13
β-strand	53-57	5	12
β-strand	60-65	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-91	8	13
β-strand	97-99	3	13
β-strand	103-108	6	13
β-strand	117-121	5	14
β-strand	122-123	2	15
β-strand	131-135	5	14
α-helix	144-146	3
β-strand	151-153	3	14
α-helix	154-156	3
β-strand	157-161	5	14
α-helix	162-164	3
β-strand	166-175	10	14
α-helix	182-184	3
β-strand	196	1	14

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-21	3	18
β-strand	22-25	4	16
β-strand	31-37	7	17
β-strand	44-51	8	17
β-strand	54-57	4	17
β-strand	64-68	5	18
β-strand	73	1	16
β-strand	74-78	5	18
α-helix	83-85	3
β-strand	87-94	8	17
α-helix	102-104	3
β-strand	105-106	2	17
β-strand	110-115	6	17
β-strand	122	1	19
α-helix	123-124	2
β-strand	125-130	6	15
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	15
β-strand	152	1	19
β-strand	156-162	7	20
β-strand	165-166	2	20
β-strand	171-173	3	15
β-strand	178-179	2	15
β-strand	189-198	10	15
α-helix	199-203	5
β-strand	208-215	8	20
β-strand	218	1	21
α-helix	229-230	2
β-strand	232	1	21
β-strand	234-241	8	20

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	22
α-helix	4-5	2
β-strand	6-11	6	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	35-41	7	24
β-strand	44-45	2	24
β-strand	50-51	2	23
α-helix	52-54	3
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-84	7	24
α-helix	90	1
β-strand	91-94	4	24

Chain G: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	25
β-strand	9-13	5	26
β-strand	18-25	8	25
β-strand	32-37	6	26
β-strand	44-49	6	26
β-strand	53-57	5	25
β-strand	60-65	6	25
β-strand	70-75	6	25
α-helix	80-82	3
β-strand	84-91	8	26
β-strand	97-99	3	26
β-strand	103-108	6	26
β-strand	117-120	4	27
α-helix	121-124	4
β-strand	130-135	6	27
α-helix	144-146	3
β-strand	151-153	3	27
α-helix	154-156	3
β-strand	157-161	5	27
α-helix	162-164	3
β-strand	166-175	10	27
α-helix	182-185	4
β-strand	196	1	27
α-helix	198-201	4

Chain H: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-14	5	29
β-strand	19-21	3	30
β-strand	22-25	4	28
β-strand	31-37	7	29
β-strand	44-51	8	29
β-strand	54-57	4	29
β-strand	65-68	4	30
β-strand	73	1	28
β-strand	74-78	5	30
α-helix	83-85	3
β-strand	87-94	8	29
α-helix	102-104	3
β-strand	105-106	2	29
β-strand	110-115	6	29
α-helix	118-120	3
β-strand	122	1	31
α-helix	123-124	2
β-strand	125-129	5	32
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	32
β-strand	152	1	31
β-strand	156-162	7	33
β-strand	165-167	3	33
β-strand	171-173	3	32
α-helix	177	1
β-strand	178-179	2	32
β-strand	189-198	10	32
α-helix	199-202	4
β-strand	208-215	8	33
β-strand	218	1	34
α-helix	229-230	2
β-strand	232	1	34
β-strand	234-241	8	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major histocompatibility complex class I-related gene protein	A, C	protein	271	Homo sapiens	Q95460 (AlphaFold model)
Beta-2-microglobulin	B, F	protein	100	Homo sapiens	P61769 (AlphaFold model)
TCR alpha chain	D, G	protein	204	Homo sapiens
TCR beta chain	E, H	protein	246	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>6PUM_1 Major histocompatibility complex class I-related gene protein (chains A, C)
MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHW
ERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDF
LIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRT
EPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQ
AWASIELDPQSSNLYSCHVEHSGVHMVLQVP

Sequence of entity 2 (B, F), FASTA

>6PUM_2 Beta-2-microglobulin (chains B, F)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D, G), FASTA

>6PUM_3 TCR alpha chain (chains D, G)
MGQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGR
FSSFLSRSKGYSYLLLKELQMKDSASYLCAVKDSNYQLIWGAGTKLIIKPDIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E, H), FASTA

>6PUM_4 TCR beta chain (chains E, H)
MNAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGE
VPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSVWTGEGSGELFFGEGSRLTVLEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
Q84	1,2-dideoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyr…	C12 H18 N4 O6	2

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

Primary citation

The molecular basis underpinning the potency and specificity of MAIT cell antigens. Awad, W., Ler, G.J.M., Xu, W. et al. Nat Immunol (2020) 21:400-411. DOI 10.1038/s41590-020-0616-6 · PubMed

Other PDB entries of the same protein (UniProt Q95460 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PUD 1.8 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-5'OH-Pentyl-5-OP-U
6PUG 1.8 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-2`OH-Ethyl-5-OP-U
6PUL 1.84 Å, Structure of human MAIT A-F7 TCR in complex with human MR1 3'D-5-OP-RU
7ZT7 1.84 Å, Structure of E8 TCR in complex in human MR1 bound to 5FSA
6PUC 1.85 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-5-OP-RU
6PUH 1.88 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-Ribityl-less
6W9U 1.89 Å, Structure of human MAIT A-F7 TCR in complex with patient MR1-R9H-Ac-6-FP
4L4V 1.9 Å, Structure of human MAIT TCR in complex with human MR1-RL-6-Me-7-OH
5U6Q 1.9 Å, Structure of human MR1-3-F-SA in complex with human MAIT A-F7 TCR
6PUE 1.9 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-4'D-5-OP-RU
6PUF 1.92 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-5'D-5-OP-RU
6PUJ 1.92 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-3`OH-Propyl-5-OP-U

Browse structure collections

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