6JTN: HLA-C08

Crystal structure of HLA-C08 in complex with a tumor mut10m peptide. Determined by X-ray diffraction at 1.9 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,579
Mol. weight: 44.23 kDa
Released: 15 Apr 2020

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

Secondary structure: helices and β-sheets

6JTN contains 15 α-helices and 30 β-strands across 2 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: 12 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	50-53	4
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
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
α-helix	225-227	3
β-strand	229-230	2	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	270-273	4	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I antigen, Cw8.2 alpha chain	A	protein	273	Homo sapiens	C1K0Y1 (AlphaFold model)
Beta-2-microglobulin	B	protein	98	Homo sapiens	P61769 (AlphaFold model)
10-mer peptide	C	protein	10	Homo sapiens	P01116 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6JTN_1 HLA class I antigen, Cw8.2 alpha chain (chains A)
SHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVQFDSDAASPRGEPRAPWVEQEGPEYWD
RETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQRMYGCDLGPDGRLLRGYNQFAYDGK
DYIALNEDLRSWTAADKAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKKTLQR
AEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTF
QKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRW

Sequence of entity 2 (B), FASTA

>6JTN_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD

Sequence of entity 3 (C), FASTA

>6JTN_3 10-mer peptide (chains C)
GADGVGKSAL

Primary citation

Immune-based mutation classification enables neoantigen prioritization and immune feature discovery in cancer immunotherapy. Bai, P., Li, Y., Zhou, Q. et al. Oncoimmunology (2021) 10:1868130-1868130. DOI 10.1080/2162402X.2020.1868130 · PubMed

Other PDB entries of the same protein (UniProt C1K0Y1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ULI 1.88 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
6JTP 1.9 Å, Crystal structure of HLA-C08 in complex with a tumor mut9m peptide
6ULK 1.9 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
6ULN 2.01 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
6ULR 3.2 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
6UON 3.5 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
9WJ6 4.54 Å, An integrated in silico-in vitro workflow for discovering high-affinity, selective…

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