1NFD: An alpha-beta T cell receptor (TCR) heterodimer

An alpha-beta T cell receptor (TCR) heterodimer in complex with an anti-TCR FAB fragment derived from a mitogenic antibody. Determined by X-ray diffraction at 2.8 Å resolution. Released 28 Jan 1998.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Mus musculus
Chains: 8
Atoms: 13,884
Mol. weight: 197.64 kDa
Ligands: NAG
Released: 28 Jan 1998

Explore 1NFD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NFD contains 38 α-helices and 197 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: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	9	1	2
β-strand	12-13	2	3
β-strand	18-20	3	1
β-strand	22-25	4	1
β-strand	30-37	9	2
β-strand	43-49	7	2
β-strand	54-57	4	1
β-strand	62-67	6	1
α-helix	68-70	3
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-94	9	2
β-strand	106	1	2
β-strand	107	1	1
β-strand	110-112	3	2
β-strand	114-115	2	3
α-helix	116	1
β-strand	124-128	5	4
β-strand	129	1	5
β-strand	139-144	6	4
β-strand	161-162	2	4
β-strand	166-169	4	6
β-strand	176-179	4	6
β-strand	181-184	4	4
β-strand	187	1	7
β-strand	189	1	7
α-helix	191-194	4

Chain B: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	8
β-strand	10-14	5	9
β-strand	20-24	5	8
β-strand	31-36	6	10
β-strand	37	1	9
β-strand	44-50	7	10
β-strand	54-57	4	10
β-strand	68-69	2	8
β-strand	75-78	4	8
α-helix	84-86	3
β-strand	88-90	3	9
β-strand	92-95	4	10
β-strand	107-108	2	10
α-helix	109	1
β-strand	112-116A	6	9
α-helix	119-121	3
β-strand	123	1	11
β-strand	126-130	5	12
β-strand	131	1	5
α-helix	132	1
α-helix	134-140	7
β-strand	142-152	11	12
β-strand	153	1	11
β-strand	157-163	7	13
β-strand	166-167	2	13
β-strand	172-174	3	12
β-strand	179-182	4	12
β-strand	189-199	11	12
α-helix	200-204	5
β-strand	210-216	7	13
β-strand	219	1	14
β-strand	233	1	14
β-strand	235-241	7	13

Chain C: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	15
β-strand	5	1	16
β-strand	11-13	3	17
β-strand	18-20	3	18
β-strand	22	1	16
β-strand	25	1	15
β-strand	30-38	10	19
β-strand	44-49	6	19
β-strand	57	1	18
β-strand	63	1	18
β-strand	67	1	20
β-strand	72	1	20
β-strand	75-77	3	18
α-helix	82-84	3
β-strand	86-94	9	19
β-strand	106	1	19
β-strand	110-111	2	19
β-strand	113-115	3	17
α-helix	116	1
β-strand	124-126	3	21
β-strand	139-144	6	21
β-strand	160-162	3	21
β-strand	166-168	3	22
β-strand	177-179	3	22
β-strand	180-184	5	21
α-helix	191-194	4
β-strand	205	1	21

Chain D: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	23
β-strand	10-14	5	24
β-strand	18-24	7	23
α-helix	25-26	2
β-strand	31-37	7	24
β-strand	43-50	8	24
β-strand	55-56	2	24
β-strand	66-69	4	23
β-strand	75-80	6	23
α-helix	84-86	3
β-strand	88-95	8	24
β-strand	107-108	2	24
β-strand	112-116A	6	24
α-helix	119-121	3
β-strand	126	1	25
β-strand	129-130	2	26
α-helix	134-139	6
β-strand	142-152	11	26
β-strand	158-163	6	27
β-strand	166-168	3	27
β-strand	172-174	3	26
β-strand	179-182	4	28
β-strand	189-191	3	28
β-strand	192-199	8	26
α-helix	200-204	5
β-strand	210-216	7	27
β-strand	219	1	29
β-strand	233	1	29
β-strand	235-241	7	27

Chain E: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	30
β-strand	9-14	5	31
β-strand	21-25	5	30
α-helix	28-30	3
β-strand	34-38	5	31
β-strand	44-48	5	31
β-strand	49	1	32
β-strand	53	1	32
α-helix	54-55	2
β-strand	62-67	6	30
β-strand	70-75	6	30
α-helix	80-82	3
β-strand	85-92	8	31
β-strand	95B-98	4	31
β-strand	102-106A	6	31
β-strand	111	1	33
β-strand	114-116	3	34
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-130	2	35
β-strand	134-139	6	34
β-strand	140	1	33
β-strand	145-150	6	36
β-strand	153-155	3	36
β-strand	160	1	37
β-strand	165	1	34
β-strand	173-177	5	34
β-strand	178	1	37
β-strand	181-182	2	35
α-helix	183-187	5
β-strand	192-197	6	36
β-strand	209	1	36

Chain F: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	38
β-strand	10-12	3	39
β-strand	17-25	9	38
α-helix	29-31	3
β-strand	32-39	8	40
β-strand	45-51	7	40
β-strand	57-59	3	40
α-helix	61-63	3
β-strand	67	1	38
β-strand	70-71	2	38
β-strand	77-82A	7	38
α-helix	84-86	3
β-strand	88-89	2	39
β-strand	91-96	6	40
β-strand	100-103	5	40
β-strand	108-111	4	39
β-strand	120	1	41
β-strand	124	1	42
β-strand	137-139	3	43
β-strand	141	1	42
β-strand	144-147	4	44
β-strand	153-154	2	45
α-helix	162-164	3
β-strand	171-173	3	46
β-strand	178	1	44
β-strand	185-187	3	44
β-strand	189-191	3	46
β-strand	192-194	3	43
β-strand	206-211	5	45
β-strand	219-222	4	45

Chain G: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	47
β-strand	9-14	5	48
β-strand	19-24	6	47
β-strand	33-38	6	48
β-strand	44-49	6	48
α-helix	54-55	2
β-strand	62-67	6	47
β-strand	70-75	6	47
α-helix	80-82	3
β-strand	85-92	8	48
β-strand	95B-98	4	48
β-strand	102-106A	6	48
β-strand	115-116	2	49
α-helix	119-121	3
α-helix	122-126	5
β-strand	129	1	50
β-strand	134-139	6	49
β-strand	147	1	51
β-strand	149	1	52
β-strand	150	1	53
β-strand	154	1	52
β-strand	159-160	2	54
β-strand	165-166	2	49
β-strand	172-177	6	49
β-strand	178-179	2	54
β-strand	182	1	50
α-helix	183-186	4
β-strand	192	1	53
β-strand	195	1	51

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	55
β-strand	11-12	2	56
β-strand	18-25	8	55
α-helix	29-31	3
β-strand	33-39	7	57
β-strand	45-51	7	57
β-strand	57-59	3	57
α-helix	61-63	3
β-strand	67-72	6	55
β-strand	77-82	6	55
α-helix	84-86	3
β-strand	88-89	2	58
β-strand	91-95	5	57
β-strand	100	1	57
β-strand	108-109	2	58
β-strand	110-111	2	56
β-strand	120-124	5	59
β-strand	137-147	11	59
β-strand	153-157	4	60
α-helix	162-164	3
β-strand	171-173	3	59
α-helix	174-176	3
β-strand	179	1	61
β-strand	184	1	61
β-strand	185-194	10	59
β-strand	206-211	5	60
β-strand	221-222	2	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N15 alpha-beta T-cell receptor	A, C	protein	203	Mus musculus	P01849 (AlphaFold model)
N15 alpha-beta T-cell receptor	B, D	protein	239	Mus musculus	P01852 (AlphaFold model)
H57 FAB	E, G	protein	212	Mus musculus
H57 FAB	F, H	protein	222	Mus musculus

Sequence of entity 1 (A, C), FASTA

>1NFD_1 N15 ALPHA-BETA T-CELL RECEPTOR (chains A, C)
DSVTQTEGLVTVTEGLPVKLNCTYQTTYLTIAFFWYVQYLNEAPQVLLKSSTDNKRTEHQ
GFHATLHKSSSSFHLQKSSAQLSDSALYYCALSEGGNYKYVFGAGTRLKVIAHIQNPEPA
VYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKTVLDMKAMDSKSNGAIAWSNQ
TSFTCQDIFKETNATYPSSDVPC

Sequence of entity 2 (B, D), FASTA

>1NFD_2 N15 ALPHA-BETA T-CELL RECEPTOR (chains B, D)
DSGVVQSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLIQHYEKVERDKGFL
PSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLRWGDEQYFGPGTRLTVLEDLRNVTP
PKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNY
SYSLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADC

Sequence of entity 3 (E, G), FASTA

>1NFD_3 H57 FAB (chains E, G)
YELIQPSSASVTVGETVKITCSGDQLPKNFAYWFQQKSDKNILLLIYMDNKRPSGIPERF
SGSTSGTTATLTISGAQPEDEAAYYCLSSYGDNNDLVFGSGTQLTVLRGPKSSPKVTVFP
PSPEELRTNKATLVCLVNDFYPGSATVTWKANGATINDGVKTTKPSKQGQNYMTSSYLSL
TADQWKSHNRVSCQVTHEGETVEKSLSPAECL

Sequence of entity 4 (F, H), FASTA

>1NFD_4 H57 FAB (chains F, H)
EVYLVESGGDLVQPGSSLKVSCAASGFTFSDFWMYWVRQAPGKGLEWVGRIKNIPNNYAT
EYADSVRGRFTISRDDSRNSIYLQMNRLRVDDTAIYYCTRAGRFDHFDYWGQGTMVTVSS
ATTTAPSVYPLAPACDSTTSTTDTVTLGCLVKGYFPEPVTVSWNSGALTSGVHTFPSVLH
SGLYSLSSSVTVPSSTWPKQPITCNVAHPASSTKVDKKIEPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	14

Primary citation

Atomic structure of an alphabeta T cell receptor (TCR) heterodimer in complex with an anti-TCR fab fragment derived from a mitogenic antibody. Wang, J., Lim, K., Smolyar, A. et al. EMBO J (1998) 17:10-26. DOI 10.1093/emboj/17.1.10 · PubMed

Other PDB entries of the same protein (UniProt P01849 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
2Q86 1.85 Å, Structure of the mouse invariant NKT cell receptor Valpha14
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
5M01 1.95 Å, Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from…
1LP9 2.0 Å, Xenoreactive complex AHIII 12.2 TCR bound to p1049/HLA-A2.1
8WTE 2.17 Å, Crystal structure of TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide…
8WUL 2.36 Å, Crystal structure of affinity enhanced TCR in complex with HLA-A*11:01 bound to…
2JCC 2.5 Å, AH3 recognition of mutant HLA-A2 W167A
2J8U 2.88 Å, Large CDR3a loop alteration as a function of MHC mutation.
3MBE 2.89 Å, TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)
3C6L 3.4 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR 2W20
6MF8 TCR alpha transmembrane domain

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