7NDT: UL40:01 TCR

UL40:01 TCR in complex with HLA-E with a non-natural amino acid. Determined by X-ray diffraction at 3.0 Å resolution. Released 26 Jan 2022.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,024
Mol. weight: 188.93 kDa
Released: 26 Jan 2022

Explore 7NDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NDT contains 48 α-helices and 136 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 AAA: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
α-helix	181-182	2
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-192	7	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	233-234	2	3
β-strand	238-239	2	3
β-strand	245-254	10	3
α-helix	258-260	3
β-strand	261-266	6	4
β-strand	274-276	3	4

Chain BBB: 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	45	1	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	78-84	7	7
β-strand	91-94	4	7

Chain DDD: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	10-14	5	9
β-strand	19-24	6	8
β-strand	37-44	8	9
β-strand	51-56	6	9
β-strand	66-67	2	8
β-strand	77-80	4	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-108	9	9
α-helix	115-117	3
β-strand	122-127	6	9
β-strand	136-139	4	10
α-helix	140	1
β-strand	141-142	2	11
β-strand	151-154	4	10
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-179	4	10
α-helix	181-183	3
β-strand	186-194	9	10

Chain EEE: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
α-helix	25-26	2
β-strand	38-45	8	13
β-strand	51-57	7	13
β-strand	64-67	4	13
β-strand	76-79	4	12
β-strand	87-91	5	12
α-helix	96-98	3
β-strand	100-107	8	13
β-strand	117-118	2	13
β-strand	122-127	6	13
α-helix	131-133	3
β-strand	135	1	14
α-helix	136-137	2
β-strand	138-143	6	11
α-helix	144-145	2
α-helix	146-151	6
β-strand	154-164	11	11
β-strand	165	1	14
β-strand	169-175	7	15
β-strand	178-180	3	15
β-strand	184-186	3	11
α-helix	190	1
β-strand	191	1	11
α-helix	200-201	2
β-strand	202-211	10	11
α-helix	212-216	5
β-strand	221-228	8	15
β-strand	247-254	8	15

Chain FFF: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	16
β-strand	21-28	8	16
β-strand	31-37	7	16
β-strand	46-47	2	16
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	16
β-strand	109-118	10	16
β-strand	121-126	6	16
β-strand	133-135	3	16
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
α-helix	181-182	2
β-strand	183	1	17
α-helix	184-185	2
β-strand	186-192	7	18
β-strand	200-208	9	18
β-strand	209	1	17
β-strand	214-219	6	19
β-strand	234-235	2	18
β-strand	239-240	2	18
β-strand	246-253	8	18
β-strand	262-267	6	19
β-strand	275-277	3	19

Chain GGG: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	20
β-strand	6-11	6	21
β-strand	21-30	10	21
β-strand	31	1	20
β-strand	35-41	7	22
β-strand	45	1	22
β-strand	50-51	2	21
α-helix	52-54	3
β-strand	55-56	2	21
β-strand	62-70	9	21
β-strand	78-84	7	22
α-helix	90	1
β-strand	91-94	4	22

Chain III: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	23
β-strand	10-14	5	24
β-strand	19-24	6	23
β-strand	37-44	8	24
β-strand	51-56	6	24
β-strand	66-67	2	23
β-strand	77-80	4	23
β-strand	86-91	6	23
α-helix	96-98	3
β-strand	100-108	9	24
β-strand	122-127	6	24
β-strand	136-140	5	25
β-strand	141-142	2	26
β-strand	150-156	7	25
β-strand	170-172	3	25
α-helix	173-175	3
β-strand	176-179	4	25
α-helix	181-183	3
β-strand	186-194	9	25

Chain JJJ: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	27
β-strand	10-14	5	28
β-strand	19-24	6	27
β-strand	38-45	8	28
β-strand	51-57	7	28
β-strand	64-67	4	28
β-strand	76-79	4	27
β-strand	87-91	5	27
α-helix	96-98	3
β-strand	100-106	7	28
β-strand	117-118	2	28
β-strand	122-127	6	28
α-helix	131-133	3
β-strand	135	1	29
α-helix	136-137	2
β-strand	138-143	6	26
α-helix	144-145	2
α-helix	146-152	7
β-strand	154-164	11	26
β-strand	165	1	29
β-strand	169-175	7	30
β-strand	178-180	3	30
β-strand	184-186	3	26
α-helix	190	1
β-strand	191-192	2	26
α-helix	200-201	2
β-strand	202-211	10	26
α-helix	212-216	5
β-strand	221-228	8	30
β-strand	231	1	31
β-strand	245	1	31
β-strand	247-254	8	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	AAA, FFF	protein	277	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	BBB, GGG	protein	100	Homo sapiens	P61769 (AlphaFold model)
UL40(15-23 H4C)	CCC, HHH	protein	9	Homo sapiens
T cell receptor alpha variable 26-1,T cell receptor alpha joining 37,T cell receptor alpha chain…	DDD, III	protein	198	Homo sapiens	A0A087WT03 (AlphaFold model), A0A087X096, P01848
T cell receptor beta variable 14,T cell receptor beta joining 2-3,T cell receptor beta constant 2	EEE, JJJ	protein	243	Homo sapiens	A0A0B4J200, A0A5B0, A0A5B9

Sequence of entity 1 (AAA, FFF), FASTA

>7NDT_1 HLA class I histocompatibility antigen, alpha chain E (chains AAA, FFF)
MGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEY
WDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQCAYD
GKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETL
LHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (BBB, GGG), FASTA

>7NDT_2 Beta-2-microglobulin (chains BBB, GGG)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (CCC, HHH), FASTA

>7NDT_3 UL40(15-23 H4C) (chains CCC, HHH)
VMAPRTLIL

Sequence of entity 4 (DDD, III), FASTA

>7NDT_4 T cell receptor alpha variable 26-1,T cell receptor alpha joining 37,T cell receptor alpha chain constant (chains DDD, III)
MAAKTTQPPSMDVAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEM
ASLIITEDRKSSTLILPHATLRDTAVYYCIVVRSSNTGKLIFGQGTTLQVKPDIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDT

Sequence of entity 5 (EEE, JJJ), FASTA

>7NDT_5 T cell receptor beta variable 14,T cell receptor beta joining 2-3,T cell receptor beta constant 2 (chains EEE, JJJ)
MEAGVTQFPSHSVIEKGQTVTLRCDPISGHDNLYWYRRVMGKEIKFLLHFVKESKQDESG
MPNNRFLAERTGGTYSTLKVQPAELEDSGVYFCASSQDRDTQYFGPGTRLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. Barber, C., De Souza, V.A., Paterson, R.L. et al. Eur J Immunol (2022) 52:618-632. DOI 10.1002/eji.202149745 · PubMed

Other PDB entries of the same protein (UniProt P13747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P4B 1.72 Å, HLA-E*01:03 in complex with IL9
7BH8 1.8 Å, 3H4-Fab HLA-E-VL9 co-complex
7P49 2.05 Å, HLA-E*01:03 in complex with Mtb14
6GH1 2.1 Å, HLA-E*01:03 in complex with Mtb44
9NW7 2.1 Å, CA117v2v8 Fab bound to HLA-E-VL9
6GH4 2.16 Å, HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln.
6ZKX 2.17 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG)
8RLT 2.25 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide
6ZKW 2.26 Å, Crystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61)
6ZKZ 2.3 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C)
9NW8 2.3 Å, CA117v2v8 Fab bound to HLA-E-Mtb44
9NW9 2.3 Å, CA117v2v8 Fab bound to HLA-E-RL9HIV

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