4PJE: Human MR1-Ac-6-FP

Structure of human MR1-Ac-6-FP in complex with human MAIT B-B10 TCR. Determined by X-ray diffraction at 1.95 Å resolution. Released 2 Jul 2014.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,211
Mol. weight: 189.76 kDa
Ligands: 30W
Released: 2 Jul 2014

Explore 4PJE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PJE contains 56 α-helices and 146 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	22-28	7	1
β-strand	31-37	7	1
β-strand	44-45	2	1
α-helix	48-53	6
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	183-190	8	3
β-strand	196-205	10	3
β-strand	206	1	2
β-strand	211-216	6	4
β-strand	219-220	2	4
α-helix	224-225	2
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

Chains B and D: 4 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
α-helix	90	1
β-strand	91-94	4	7

Chain C: 10 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	183-187	5	10
β-strand	198-205	8	10
β-strand	206	1	9
β-strand	211-216	6	11
β-strand	219	1	11
β-strand	226-227	2	10
α-helix	228-230	3
β-strand	231-232	2	10
β-strand	238-244	7	10
β-strand	254-260	7	11
β-strand	263-268	6	11

Chain E: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	15
β-strand	9-13	5	11
β-strand	18-25	8	15
β-strand	32-37	6	11
β-strand	44-49	6	11
β-strand	53-57	5	15
β-strand	60-65	6	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	84-91	8	11
β-strand	97-99	3	11
β-strand	103-108	6	11
β-strand	117-120	4	16
β-strand	132-135	4	16
α-helix	144-146	3
β-strand	152-153	2	16
α-helix	154-156	3
β-strand	157-161	5	16
α-helix	162-164	3
β-strand	166-174	9	16
α-helix	182-185	4
β-strand	196	1	16

Chain F: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-14	5	18
β-strand	19-21	3	19
β-strand	22-25	4	17
β-strand	31-37	7	18
β-strand	44-51	8	18
β-strand	54-57	4	18
β-strand	64-68	5	19
β-strand	73	1	17
β-strand	74-78	5	19
α-helix	83-85	3
β-strand	87-94	8	18
α-helix	100-102	3
β-strand	103-104	2	18
β-strand	108-113	6	18
β-strand	120	1	20
α-helix	121-122	2
β-strand	123-127	5	21
α-helix	128-130	3
α-helix	131-137	7
β-strand	139-149	11	21
β-strand	150	1	20
β-strand	154-160	7	22
β-strand	163-165	3	22
β-strand	169-171	3	21
α-helix	175	1
β-strand	176-177	2	21
β-strand	187-196	10	21
α-helix	197-201	5
β-strand	206-213	8	22
β-strand	216	1	23
α-helix	227-228	2
β-strand	230	1	23
β-strand	232-239	8	22

Chain G: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	24
β-strand	9-13	5	25
β-strand	18-25	8	24
β-strand	31-37	7	25
β-strand	44-49	6	25
β-strand	53-57	5	24
β-strand	60-65	6	24
β-strand	70-75	6	24
α-helix	80-82	3
β-strand	84-91	8	25
β-strand	97-99	3	25
β-strand	103-108	6	25
β-strand	117-120	4	26
α-helix	121-124	4
β-strand	130-135	6	26
α-helix	144-146	3
β-strand	152-153	2	26
α-helix	154-156	3
β-strand	157-161	5	26
α-helix	162-164	3
β-strand	166-175	10	26
α-helix	182-185	4
β-strand	196	1	26

Chain H: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10-14	5	28
β-strand	19-21	3	29
β-strand	22-25	4	27
β-strand	31-37	7	28
β-strand	44-51	8	28
β-strand	54-57	4	28
β-strand	64-68	5	29
β-strand	73	1	27
β-strand	74-78	5	29
α-helix	83-85	3
β-strand	87-94	8	28
α-helix	100-102	3
β-strand	103-104	2	28
β-strand	108-113	6	28
α-helix	116-118	3
β-strand	120	1	30
α-helix	121-122	2
β-strand	123-127	5	31
α-helix	128-130	3
α-helix	131-137	7
β-strand	139-149	11	31
β-strand	150	1	30
β-strand	154-160	7	32
β-strand	163-165	3	32
β-strand	169-171	3	31
α-helix	175	1
β-strand	176-177	2	31
β-strand	187-196	10	31
α-helix	197-200	4
β-strand	206-213	8	32
β-strand	216	1	33
α-helix	227-228	2
β-strand	230	1	33
β-strand	232-239	8	32

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, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
TCR-alpha	E, G	protein	205	Homo sapiens
TCR-beta	F, H	protein	245	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>4PJE_1 Major histocompatibility complex class I-related gene protein (chains A, C)
MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHW
ERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDF
LIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRT
EPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQ
AWASIELDPQSSNLYSCHVEHSGVHMVLQVP

Sequence of entity 2 (B, D), FASTA

>4PJE_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, G), FASTA

>4PJE_3 TCR-alpha (chains E, G)
HMGQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKG
RFSSFLSRSKGYSYLLLKELQMKDSASYLCAGMDSNYQLIWGAGTKLIIKPDIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>4PJE_4 TCR-beta (chains F, H)
HMNAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKG
EVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASTLGQEGQPQHFGEGSRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
30W	N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide	C9 H7 N5 O3	2

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

Primary citation

A molecular basis underpinning the T cell receptor heterogeneity of mucosal-associated invariant T cells. Eckle, S.B., Birkinshaw, R.W., Kostenko, L. et al. J Exp Med (2014) 211:1585-1600. DOI 10.1084/jem.20140484 · 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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