8YJ2: N17.1.2 recognition of NRAS neoantigens

N17.1.2 recognition of NRAS neoantigens. Determined by X-ray diffraction at 2.26 Å resolution. Released 4 Dec 2024.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,106
Mol. weight: 96.21 kDa
Released: 4 Dec 2024

Explore 8YJ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YJ2 contains 27 α-helices and 75 β-strands across 5 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	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	57-84	28
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	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 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
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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	15
β-strand	10-14	5	16
β-strand	19-21	3	15
β-strand	24-26	3	15
β-strand	33-39	7	16
β-strand	45-52	8	16
α-helix	56-58	3
β-strand	59-60	2	15
β-strand	63-68	6	15
β-strand	73-78	6	15
α-helix	83-85	3
β-strand	87-94	8	16
β-strand	100-102	3	16
β-strand	106-111	6	16
β-strand	120-125	6	17
β-strand	126	1	12
β-strand	133-138	6	17
α-helix	146-149	4
β-strand	154-156	3	17
α-helix	157-159	3
β-strand	160-164	5	17
α-helix	165-167	3
β-strand	169-178	10	17
α-helix	185-188	4
β-strand	199	1	17

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-21	3	10
β-strand	22-25	4	8
β-strand	31-37	7	9
β-strand	43-51	9	9
β-strand	54-57	4	9
β-strand	65-66	2	10
β-strand	73	1	8
β-strand	76-78	3	10
α-helix	83-85	3
β-strand	87-94	8	9
α-helix	103-105	3
β-strand	106-107	2	9
β-strand	111-116	6	9
β-strand	123	1	11
α-helix	124-125	2
β-strand	126-130	5	12
α-helix	131-133	3
α-helix	134-140	7
β-strand	142-152	11	12
β-strand	153	1	11
β-strand	157-163	7	13
β-strand	166-168	3	13
β-strand	172-174	3	12
β-strand	179-180	2	12
β-strand	190-199	10	12
α-helix	200-203	4
β-strand	209-216	8	13
β-strand	219	1	14
α-helix	230-231	2
β-strand	233	1	14
β-strand	235-242	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
human leukocyte antigen	A	protein	276	Homo sapiens	F6IQR9 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Ile-leu-asp-thr-ala-gly-arg-glu-glu-tyr	C	protein	10	Homo sapiens	P01116 (AlphaFold model)
tcr beta	E	protein	247	Homo sapiens	P0DTU4 (AlphaFold model)
tcr alpha	D	protein	207	Homo sapiens	P01848

Sequence of entity 1 (A), FASTA

>8YJ2_1 human leukocyte antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEY
WDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYD
GKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETL
QRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>8YJ2_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>8YJ2_3 ILE-LEU-ASP-THR-ALA-GLY-ARG-GLU-GLU-TYR (chains C)
ILDTAGREEY

Sequence of entity 4 (E), FASTA

>8YJ2_4 tcr beta (chains E)
MEAQVTQNPRYLITVTGKKLTVTCSQNMNHEYMSWYRQDPGLGLRQIYYSMNVEVTDKGD
VPEGYKVSRKEKRNFPLILESPSPNQTSLYFCASSLVSTPLPKETQYFGPGTRLLVLEDL
KNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRAD

Sequence of entity 5 (D), FASTA

>8YJ2_5 tcr alpha (chains D)
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 F6IQR9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YIV 2.1 Å, N17.1.2 recognition of NRAS neoantigens
9RU5 3.26 Å, Cryo-EM structure of TCRpub/pMHC
8T7R 3.84 Å, Crystal structure of human leukocyte antigen A*0101 in complex with the Fab of…

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