5D7J: Human MR1-5-OP-RU

Structure of human MR1-5-OP-RU in complex with human MAIT M33.64(Y95alphaF) TCR. Determined by X-ray diffraction at 1.97 Å resolution. Released 27 Jan 2016.

Method: X-ray diffraction
Resolution: 1.97 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,052
Mol. weight: 188.08 kDa
Ligands: 2LJ
Released: 27 Jan 2016

Explore 5D7J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D7J contains 50 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: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	9-13	5	2
β-strand	18-25	8	1
β-strand	32-37	6	2
β-strand	44-49	6	2
β-strand	53-57	5	1
β-strand	60-65	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-91	8	2
β-strand	97-99	3	2
β-strand	103-108	6	2
β-strand	117-120	4	3
α-helix	121-124	4
β-strand	130-135	6	3
α-helix	143-146	4
β-strand	151-153	3	3
α-helix	154-156	3
β-strand	157-161	5	3
β-strand	166-175	10	3
α-helix	182-185	4
β-strand	196	1	3

Chain B: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-14	5	5
β-strand	19-21	3	6
β-strand	22-25	4	4
β-strand	31-37	7	5
β-strand	44-49	6	5
β-strand	56-57	2	5
β-strand	64-66	3	6
β-strand	73	1	4
β-strand	76-78	3	6
α-helix	83-85	3
β-strand	87-94	8	5
α-helix	101-103	3
β-strand	104-105	2	5
β-strand	109-114	6	5
α-helix	117-119	3
β-strand	121	1	7
α-helix	122-123	2
β-strand	124-128	5	8
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	8
β-strand	151	1	7
β-strand	155-161	7	9
β-strand	164-166	3	9
β-strand	170-172	3	8
β-strand	177-178	2	8
β-strand	188-197	10	8
α-helix	198-201	4
β-strand	207-214	8	9
β-strand	217	1	10
α-helix	228-229	2
β-strand	231	1	10
β-strand	233-240	8	9

Chain C: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
β-strand	22-28	7	11
β-strand	31-37	7	11
β-strand	44-45	2	11
α-helix	48-51	4
α-helix	56-84	29
β-strand	91-100	10	11
β-strand	106-114	9	11
β-strand	117-123	7	11
β-strand	128-131	4	11
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	12
α-helix	181-182	2
β-strand	183-190	8	13
β-strand	196-205	10	13
β-strand	206	1	12
β-strand	211-216	6	14
β-strand	220	1	14
α-helix	224-225	2
β-strand	226-227	2	13
β-strand	231-232	2	13
β-strand	238-245	8	13
β-strand	254-260	7	14
β-strand	263-268	6	14

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
α-helix	4-5	2
β-strand	6-11	6	16
β-strand	21-30	10	16
β-strand	31	1	15
β-strand	36-41	6	17
β-strand	44-45	2	17
β-strand	50-51	2	16
α-helix	52-54	3
β-strand	55-56	2	16
β-strand	62-70	9	16
β-strand	78-83	6	17
β-strand	91-94	4	17

Chain E: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
α-helix	15-16	2
β-strand	22-28	7	18
β-strand	31-37	7	18
β-strand	44-45	2	18
α-helix	48-51	4
α-helix	56-84	29
β-strand	91-100	10	18
β-strand	106-114	9	18
β-strand	117-123	7	18
β-strand	128-131	4	18
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	19
α-helix	181-182	2
β-strand	183-188	6	20
β-strand	197-205	9	20
β-strand	206	1	19
β-strand	211-216	6	21
β-strand	220-221	2	21
α-helix	222	1
β-strand	226-227	2	20
α-helix	228-230	3
β-strand	231-232	2	20
β-strand	238-245	8	20
β-strand	254-260	7	21
β-strand	263-268	6	21

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
α-helix	14-15	2
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	36-41	6	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	78-83	6	24
β-strand	91-94	4	24

Chain G: 4 helices, 18 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
α-helix	100	1
β-strand	103-108	6	26
β-strand	117-120	4	27
β-strand	122-123	2	28
β-strand	132-135	4	27
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
β-strand	196	1	27

Chain H: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	29
β-strand	10-14	5	30
β-strand	19-21	3	31
β-strand	22-25	4	29
β-strand	31-37	7	30
β-strand	44-49	6	30
β-strand	56-57	2	30
β-strand	65-66	2	31
β-strand	73	1	29
β-strand	76-78	3	31
α-helix	83-85	3
β-strand	87-94	8	30
α-helix	101-103	3
β-strand	104-105	2	30
β-strand	109-114	6	30
α-helix	117-119	3
β-strand	121	1	32
α-helix	122-123	2
β-strand	124-129	6	28
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-150	11	28
β-strand	151	1	32
β-strand	155-161	7	33
β-strand	164-166	3	33
β-strand	170-172	3	28
β-strand	177-178	2	28
β-strand	188-197	10	28
α-helix	198-201	4
β-strand	207-214	8	33
β-strand	217	1	34
α-helix	228-229	2
β-strand	231	1	34
β-strand	233-240	8	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
M33.64 TCR Alpha Chain	A, G	protein	204	Homo sapiens
M33.64 TCR Beta Chain	B, H	protein	245	Homo sapiens
Major histocompatibility complex class I-related gene protein	C, E	protein	271	Homo sapiens	Q95460 (AlphaFold model)
Beta-2-microglobulin	D, F	protein	100	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, G), FASTA

>5D7J_1 M33.64 TCR Alpha Chain (chains A, G)
MGQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGR
FSSFLSRSKGYSYLLLKELQMKDSASYLCAVMDSNFQLIWGAGTKLIIKPDIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B, H), FASTA

>5D7J_2 M33.64 TCR Beta Chain (chains B, H)
MIAGITQAPTSQILAAGRRMTLRCTQDMRHNAMYWYRQDLGLGLRLIHYSNTAGTTGKGE
VPDGYSVSRANTDDFPLTLASAVPSQTSVYFCASSEAGGNTGELFFGEGSRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Sequence of entity 3 (C, E), FASTA

>5D7J_3 Major histocompatibility complex class I-related gene protein (chains C, E)
MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHW
ERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDF
LIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRT
EPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQ
AWASIELDPQSSNLYSCHVEHSGVHMVLQVP

Sequence of entity 4 (D, F), FASTA

>5D7J_4 Beta-2-microglobulin (chains D, F)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
2LJ	1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl…	C12 H20 N4 O6	2

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

Primary citation

Diversity of T Cells Restricted by the MHC Class I-Related Molecule MR1 Facilitates Differential Antigen Recognition. Gherardin, N.A., Keller, A.N., Woolley, R.E. et al. Immunity (2016) 44:32-45. DOI 10.1016/j.immuni.2015.12.005 · 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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