4NQD: PDB entry 4NQD

Crystal structure of TCR-MR1 ternary complex and non-covalently bound 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil. Determined by X-ray diffraction at 2.2 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,111
Mol. weight: 188.07 kDa
Ligands: Q87
Released: 16 Apr 2014

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

Secondary structure: helices and β-sheets

4NQD contains 48 α-helices and 149 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: 8 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	48-53	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
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	1	4
β-strand	226-227	2	3
β-strand	231-232	2	3
β-strand	238-244	7	3
β-strand	254-260	7	4
β-strand	263-268	6	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: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
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
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	226-227	2	10
α-helix	228-229	2
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 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	117-120	4	14
α-helix	121	1
β-strand	122	1	15
α-helix	123-124	2
β-strand	130-135	6	14
α-helix	143-146	4
β-strand	152-153	2	14
β-strand	157-161	5	14
β-strand	166-175	10	14
α-helix	182-185	4
β-strand	196	1	14

Chain E: 9 helices, 27 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	44-49	6	17
β-strand	56-57	2	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
α-helix	118-120	3
β-strand	122	1	19
α-helix	123-124	2
β-strand	125-129	5	20
β-strand	130	1	15
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	20
β-strand	152	1	19
β-strand	156-162	7	21
β-strand	165-167	3	21
β-strand	171-173	3	20
α-helix	177	1
β-strand	178-179	2	20
β-strand	189-198	10	20
α-helix	199-202	4
β-strand	208-215	8	21
β-strand	218	1	22
α-helix	229-230	2
β-strand	232	1	22
β-strand	234-241	8	21

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	23
α-helix	4-5	2
β-strand	6-11	6	24
β-strand	21-30	10	24
β-strand	31	1	23
β-strand	36-41	6	25
β-strand	44-45	2	25
β-strand	50-51	2	24
α-helix	52-54	3
β-strand	55-56	2	24
β-strand	62-70	9	24
β-strand	78-83	6	25
α-helix	90	1
β-strand	91-94	4	25

Chain G: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	26
β-strand	9-13	5	27
β-strand	18-25	8	26
β-strand	32-37	6	27
β-strand	44-49	6	27
β-strand	53-57	5	26
β-strand	60-65	6	26
β-strand	70-75	6	26
α-helix	80-82	3
β-strand	84-91	8	27
β-strand	97-99	3	27
β-strand	103-108	6	27
α-helix	109	1
β-strand	117-121	5	28
β-strand	122	1	29
β-strand	131-135	5	28
α-helix	143-145	3
β-strand	151-153	3	28
α-helix	154-156	3
β-strand	157-161	5	28
α-helix	162-164	3
β-strand	166-175	10	28
β-strand	196	1	28

Chain H: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	30
β-strand	10-14	5	31
β-strand	19-21	3	32
β-strand	22-25	4	30
β-strand	31-37	7	31
β-strand	44-49	6	31
β-strand	56-57	2	31
β-strand	64-68	5	32
β-strand	73	1	30
β-strand	74-78	5	32
α-helix	83-85	3
β-strand	87-94	8	31
β-strand	105-106	2	31
β-strand	110-115	6	31
β-strand	122	1	33
α-helix	123-124	2
β-strand	125-129	5	34
β-strand	130	1	29
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	34
β-strand	152	1	33
β-strand	156-162	7	35
β-strand	165-167	3	35
β-strand	171-173	3	34
α-helix	177	1
β-strand	178-179	2	34
β-strand	189-198	10	34
α-helix	199-203	5
β-strand	208-215	8	35
β-strand	218	1	36
α-helix	229-230	2
β-strand	232	1	36
β-strand	234-241	8	35

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	99	Homo sapiens	P61769 (AlphaFold model)
TCR alpha chain	D, G	protein	203	Homo sapiens	Q6P4G7 (AlphaFold model)
TCR beta chain	E, H	protein	245	Homo sapiens	P01850 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4NQD_1 Major histocompatibility complex class I-related gene protein (chains A, C)
MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHW
ERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDF
LIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRT
EPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQ
AWASIELDPQSSNLYSCHVEHSGVHMVLQVP

Sequence of entity 2 (B, F), FASTA

>4NQD_2 Beta-2-microglobulin (chains B, F)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D, G), FASTA

>4NQD_3 TCR alpha chain (chains D, G)
GQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRF
SSFLSRSKGYSYLLLKELQMKDSASYLCAVKDSNYQLIWGAGTKLIIKPDIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E, H), FASTA

>4NQD_4 TCR beta chain (chains E, H)
NAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEV
PNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSVWTGEGSGELFFGEGSRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
Q87	1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimid…	C12 H18 N4 O7	2

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

Primary citation

T-cell activation by transitory neo-antigens derived from distinct microbial pathways. Corbett, A.J., Eckle, S.B., Birkinshaw, R.W. et al. Nature (2014) 509:361-365. DOI 10.1038/nature13160 · 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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