8Y6X: PDB entry 8Y6X

Crystal structure of ternary complex of human MR1, ligand #4, and MAIT-TCR A-F7. Determined by X-ray diffraction at 3.4 Å resolution. Released 30 Oct 2024.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,487
Mol. weight: 94.16 kDa
Ligands: A1LXU
Released: 30 Oct 2024

Explore 8Y6X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y6X contains 22 α-helices and 74 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: 9 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	134-145	12
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	220	1	4
β-strand	225-227	3	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
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	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	78-84	7	7
α-helix	90	1
β-strand	91-94	4	7

Chain D: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	8
β-strand	9-13	5	9
β-strand	18-25	8	8
β-strand	32-37	6	9
β-strand	44-49	6	9
β-strand	53-57	5	8
β-strand	60-65	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-91	8	9
α-helix	96	1
β-strand	97-99	3	9
α-helix	100	1
β-strand	103-108	6	9
β-strand	117-122	6	10
β-strand	123	1	11
β-strand	130-135	6	10
α-helix	144-146	3
β-strand	151-153	3	10
β-strand	157-161	5	10
β-strand	166-175	10	10
β-strand	196	1	10

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	31-38	8	13
β-strand	41-51	11	13
β-strand	54-57	4	13
β-strand	65-68	4	14
β-strand	73	1	12
β-strand	74-78	5	14
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	105-106	2	13
β-strand	110-115	6	13
α-helix	118-120	3
β-strand	122	1	15
β-strand	125-129	5	11
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	11
β-strand	152	1	15
β-strand	156-162	7	16
β-strand	165-167	3	16
β-strand	171-173	3	11
α-helix	177	1
β-strand	178-179	2	11
β-strand	189-198	10	11
α-helix	199-203	5
β-strand	208-215	8	16
β-strand	218	1	17
α-helix	229-230	2
β-strand	232	1	17
β-strand	234-241	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major histocompatibility complex class I-related gene protein	A	protein	271	Homo sapiens	Q95460 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
MAIT T cell receptor (A-F7) alpha chain	D	protein	203	Homo sapiens	P01848 (AlphaFold model)
MAIT T cell receptor (A-F7) beta chain	E	protein	245	Homo sapiens	P0DTU4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8Y6X_1 Major histocompatibility complex class I-related gene protein (chains A)
MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHW
ERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDF
LIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRT
EPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQ
AWASIELDPQSSNLYSCHVEHSGVHMVLQVP

Sequence of entity 2 (B), FASTA

>8Y6X_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D), FASTA

>8Y6X_3 MAIT T cell receptor (A-F7) alpha chain (chains D)
GQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRF
SSFLSRSKGYSYLLLKELQMKDSASYLCAVKDSNYQLIWGAGTKLIIKPDIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E), FASTA

>8Y6X_4 MAIT T cell receptor (A-F7) beta chain (chains E)
NAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEV
PNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSVWTGEGSGELFFGEGSRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
A1LXU	5-(2-oxidanylidenepropyl)-8-[(2~{S},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pent…	C14 H20 N4 O8	1

Primary citation

Development of Ribityllumazine Analogue as Mucosal-Associated Invariant T Cell Ligands. Takasaki, R., Ito, E., Nagae, M. et al. J Am Chem Soc (2024) 146:29964-29976. DOI 10.1021/jacs.4c12997 · 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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