8YJ3: N17.1.2 recognition of NRAS neoantigens

N17.1.2 recognition of NRAS neoantigens. Determined by X-ray diffraction at 3.5 Å resolution. Released 4 Dec 2024.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,248
Mol. weight: 205.05 kDa
Released: 4 Dec 2024

Explore 8YJ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YJ3 contains 47 α-helices and 180 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: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-21	3	13
β-strand	22-24	3	11
β-strand	31-37	7	12
β-strand	43-51	9	12
β-strand	54-57	4	12
β-strand	64-66	3	13
β-strand	73	1	11
β-strand	76-78	3	13
α-helix	83-85	3
β-strand	87-94	8	12
β-strand	106-107	2	12
β-strand	111-116	6	12
β-strand	123	1	14
α-helix	124-125	2
β-strand	126-130	5	15
α-helix	131-133	3
α-helix	134-140	7
β-strand	142-152	11	15
β-strand	153	1	14
β-strand	157-163	7	16
β-strand	166-167	2	16
β-strand	172-174	3	15
α-helix	178	1
β-strand	179-180	2	15
β-strand	190-199	10	15
α-helix	200-203	4
β-strand	209-216	8	16
β-strand	219	1	17
α-helix	230-231	2
β-strand	233	1	17
β-strand	235-242	8	16

Chains B, D, F and H: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	18
β-strand	10-14	5	19
β-strand	19-21	3	18
β-strand	24-26	3	18
β-strand	33-39	7	19
β-strand	45-52	8	19
β-strand	59-60	2	18
β-strand	63-68	6	18
β-strand	73-78	6	18
α-helix	83-85	3
β-strand	87-94	8	19
β-strand	100-102	3	19
β-strand	106-111	6	19
α-helix	112	1
β-strand	120-125	6	20
β-strand	126	1	15
β-strand	133-138	6	20
β-strand	154-156	3	20
α-helix	157-159	3
β-strand	160-164	5	20
α-helix	165-167	3
β-strand	169-178	10	20
α-helix	185-188	4
β-strand	199	1	20

Chain C: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	21
β-strand	10-14	5	22
β-strand	19-21	3	23
β-strand	22-24	3	21
β-strand	31-37	7	22
β-strand	43-49	7	22
β-strand	56-57	2	22
β-strand	65-66	2	23
β-strand	73	1	21
β-strand	76-78	3	23
α-helix	83-85	3
β-strand	87-94	8	22
β-strand	105-107	3	22
β-strand	111-116	6	22
β-strand	123	1	24
α-helix	124-125	2
β-strand	126-130	5	25
α-helix	131-133	3
α-helix	134-140	7
β-strand	142-152	11	25
β-strand	153	1	24
β-strand	157-163	7	26
β-strand	166-168	3	26
β-strand	172-174	3	25
α-helix	178	1
β-strand	179-180	2	25
β-strand	190-199	10	25
α-helix	200-203	4
β-strand	209-216	8	26
β-strand	219	1	27
α-helix	230-231	2
β-strand	233	1	27
β-strand	235-242	8	26

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-21	3	3
β-strand	22-25	4	1
β-strand	31-37	7	2
β-strand	43-51	9	2
β-strand	54-57	4	2
β-strand	64-66	3	3
β-strand	73	1	1
β-strand	76-78	3	3
α-helix	83-85	3
β-strand	87-94	8	2
β-strand	105-107	3	2
β-strand	111-116	6	2
β-strand	123	1	4
α-helix	124-125	2
β-strand	126-130	5	5
α-helix	131-133	3
α-helix	134-140	7
β-strand	142-152	11	5
β-strand	153	1	4
β-strand	157-163	7	6
β-strand	166-168	3	6
β-strand	172-174	3	5
α-helix	178	1
β-strand	179-180	2	5
β-strand	190-199	10	5
α-helix	200-203	4
β-strand	209-216	8	6
β-strand	219	1	7
α-helix	230-231	2
β-strand	233	1	7
β-strand	235-242	8	6

Chain G: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	31
β-strand	10-14	5	32
β-strand	19-21	3	33
β-strand	22-25	4	31
β-strand	31-37	7	32
β-strand	43-51	9	32
β-strand	54-57	4	32
β-strand	65-66	2	33
β-strand	73	1	31
β-strand	76-78	3	33
α-helix	83-85	3
β-strand	87-94	8	32
β-strand	105-107	3	32
β-strand	111-116	6	32
β-strand	123	1	34
β-strand	126-130	5	35
α-helix	131-133	3
α-helix	134-140	7
β-strand	142-152	11	35
β-strand	153	1	34
β-strand	157-163	7	36
β-strand	166-167	2	36
β-strand	172-174	3	35
α-helix	178	1
β-strand	179-180	2	35
β-strand	190-199	10	35
α-helix	200-203	4
β-strand	209-216	8	36
β-strand	219	1	37
α-helix	230-231	2
β-strand	233	1	37
β-strand	235-242	8	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
tcr beta	A, C, E, G	protein	247	Homo sapiens	P0DTU4 (AlphaFold model)
tcr alpha	B, D, F, H	protein	207	Homo sapiens	P01848 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>8YJ3_1 tcr beta (chains A, C, E, G)
MEAQVTQNPRYLITVTGKKLTVTCSQNMNHEYMSWYRQDPGLGLRQIYYSMNVEVTDKGD
VPEGYKVSRKEKRNFPLILESPSPNQTSLYFCASSLVSTPLPKETQYFGPGTRLLVLEDL
KNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRAD

Sequence of entity 2 (B, D, F, H), FASTA

>8YJ3_2 tcr alpha (chains B, D, F, H)
MAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAK
SGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGDTAGKSTFGDGTTLTVKPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Primary citation

Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens. Wu, D., Yin, R., Chen, G. et al. Sci Adv (2024) 10:eadq6150-eadq6150. DOI 10.1126/sciadv.adq6150 · PubMed

Other PDB entries of the same protein (UniProt P0DTU4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YIV 2.1 Å, N17.1.2 recognition of NRAS neoantigens
8RLT 2.25 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide
8YJ2 2.26 Å, N17.1.2 recognition of NRAS neoantigens
8RLU 2.35 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 S3N peptide
8RLV 2.61 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 L6I peptide
8T4Z 2.69 Å, T-cell receptor and lipid complex structure
9HI7 2.81 Å, Structure of MC.7.G5 T cell receptor in complex with MR1 R9H
8TW6 3.1 Å, TCR in nanodisc ND-II
2PO6 3.2 Å, Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15…
8TW4 3.3 Å, TCR in nanodisc ND-I
8Y6X 3.4 Å, Crystal structure of ternary complex of human MR1, ligand #4, and MAIT-TCR A-F7
9C3E 3.5 Å, TCR - CD3 complex bound to HLA

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