6UK4: MHC class I antigen

Complex of T cell Receptor with HHAT Neoantigen Peptide KQWLVWLFL Presented by HLA-A206. Determined by X-ray diffraction at 2.7 Å resolution. Released 19 Aug 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,728
Mol. weight: 96.44 kDa
Released: 19 Aug 2020

Explore 6UK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UK4 contains 26 α-helices and 72 β-strands across 4 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	3-14	12	1
β-strand	18-28	11	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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
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	213-219	7	4
β-strand	222-223	2	4
α-helix	225-227	3
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	257-263	7	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	35-41	7	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
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 D: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
β-strand	11-15	5	9
β-strand	20-22	3	8
β-strand	25-27	3	8
β-strand	34-40	7	9
β-strand	47-53	7	9
β-strand	65-70	6	8
β-strand	75-80	6	8
α-helix	85-87	3
β-strand	89-96	8	9
β-strand	103-104	2	9
α-helix	105	1
β-strand	108-113	6	9
β-strand	122-127	6	10
β-strand	128	1	11
β-strand	135-140	6	10
α-helix	148-151	4
β-strand	157-158	2	10
α-helix	159-161	3
β-strand	162-166	5	10
β-strand	171-180	10	10
β-strand	201	1	10

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	12
β-strand	11-15	5	13
β-strand	20-25	6	12
α-helix	26-27	2
β-strand	32-38	7	13
β-strand	45-51	7	13
β-strand	54-57	4	13
β-strand	66-72	7	12
β-strand	75-80	6	12
α-helix	85-87	3
β-strand	90-96	7	13
α-helix	103-104	2
β-strand	105-106	2	13
β-strand	110-115	6	13
α-helix	118-120	3
β-strand	122	1	14
α-helix	123-124	2
β-strand	125-129	5	11
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	11
β-strand	152	1	14
β-strand	156-162	7	15
β-strand	165-167	3	15
β-strand	171-173	3	11
β-strand	178-179	2	11
α-helix	187-188	2
β-strand	189-198	10	11
α-helix	199-202	4
β-strand	208-215	8	15
β-strand	218	1	16
β-strand	232	1	16
β-strand	234-241	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	U5YJP1 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Protein-cysteine N-palmitoyltransferase HHAT	C	protein	9	Homo sapiens	Q5VTY9 (AlphaFold model)
302 TIL T cell receptor alpha chain	D	protein	208	Homo sapiens
302 TIL T cell receptor beta chain	E	protein	245	Homo sapiens

Sequence of entity 1 (A), FASTA

>6UK4_1 MHC class I antigen (chains A)
MGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>6UK4_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6UK4_3 Protein-cysteine N-palmitoyltransferase HHAT (chains C)
KQWLVWLFL

Sequence of entity 4 (D), FASTA

>6UK4_4 302 TIL T cell receptor alpha chain (chains D)
MAQTVTQSQPEMSVQEAETVTLSCTYDTSESDYYLFWYKQPPSRQMILVIRQEAYKQQNA
TENRFSVNFQKAAKSFSLKISDSQLGDAAMYFCAFMDSNYQLIWGAGTKLIIKPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6UK4_5 302 TIL T cell receptor beta chain (chains E)
MDAGVIQSPRHEVTEMGQEVTLRCKPISGHNSLFWYRQTMMRGLELLIYFNNNVPIDDSG
MPEDRFSAKMPNASFSTLKIQPSEPRDSAVYFCASSRTSPTDTQYFGPGTRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Primary citation

Structural dissimilarity from self drives neoepitope escape from immune tolerance. Devlin, J.R., Alonso, J.A., Ayres, C.M. et al. Nat Chem Biol (2020) 16:1269-1276. DOI 10.1038/s41589-020-0610-1 · PubMed

Other PDB entries of the same protein (UniProt U5YJP1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UJO 2.25 Å, HHAT L75F Neoantigen Peptide KQWLVWLFL Presented by HLA-A206
6UJQ 2.55 Å, HHAT Wild Type Peptide KQWLVWLLL Presented by HLA-A206
6UK2 3.14 Å, Complex of T cell Receptor with HHAT Wild Type Peptide KQWLVWLLL Presented by HLA-A206

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