6AVF: KFJ5 TCR-NY-ESO-1-HLA-B*07:02 complex

Crystal structure of the KFJ5 TCR-NY-ESO-1-HLA-B*07:02 complex. Determined by X-ray diffraction at 2.03 Å resolution. Released 28 Feb 2018.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,027
Mol. weight: 104.69 kDa
Released: 28 Feb 2018

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

Secondary structure: helices and β-sheets

6AVF contains 26 α-helices and 74 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: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	4
β-strand	11-15	5	5
β-strand	20-25	6	4
β-strand	34-40	7	5
β-strand	47-52	6	5
β-strand	57-58	2	4
β-strand	63-65	3	4
β-strand	72-77	6	4
α-helix	82-84	3
β-strand	86-93	8	5
β-strand	95-96	2	6
β-strand	99-100	2	6
β-strand	105	1	7
β-strand	108-113	6	5
α-helix	114	1
β-strand	122-127	6	8
β-strand	128	1	9
β-strand	135-140	6	8
α-helix	146-151	6
β-strand	156-158	3	8
α-helix	159-161	3
β-strand	162-166	5	8
α-helix	167-169	3
β-strand	171-180	10	8
α-helix	187-190	4
β-strand	201	1	8

Chain B: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	10
β-strand	10-14	5	7
β-strand	19-21	3	10
β-strand	23-25	3	10
β-strand	31-38	8	7
β-strand	42-49	8	7
β-strand	56-57	2	7
β-strand	64-70	7	10
β-strand	73-78	6	10
α-helix	83-85	3
β-strand	87-95	9	7
β-strand	98-104	7	7
β-strand	108-113	6	7
α-helix	116-118	3
β-strand	120	1	11
α-helix	121-122	2
β-strand	123-127	5	9
α-helix	128-130	3
α-helix	131-137	7
β-strand	139-149	11	9
β-strand	150	1	11
β-strand	154-160	7	12
β-strand	163-165	3	12
β-strand	169-171	3	9
β-strand	176-177	2	9
β-strand	187-196	10	9
α-helix	197-200	4
β-strand	206-213	8	12
β-strand	216	1	13
α-helix	227-228	2
β-strand	230	1	13
β-strand	232-239	8	12

Chain H: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	14
α-helix	20	1
β-strand	21-28	8	14
β-strand	31-37	7	14
β-strand	46-47	2	14
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	14
β-strand	109-118	10	14
β-strand	121-126	6	14
β-strand	133-135	3	14
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	15
α-helix	184-185	2
β-strand	186-193	8	16
β-strand	198-208	11	16
β-strand	209	1	15
β-strand	214-217	4	17
β-strand	228-230	3	16
α-helix	231-233	3
β-strand	234-235	2	16
β-strand	241-250	10	16
α-helix	254-256	3
β-strand	259-262	4	17
β-strand	270-272	3	17

Chain M: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
α-helix	4-5	2
β-strand	6-11	6	2
β-strand	23-30	8	2
β-strand	31	1	1
β-strand	36-41	6	3
β-strand	44-45	2	3
β-strand	50-51	2	2
α-helix	52-54	3
β-strand	55-56	2	2
β-strand	62-67	6	2
β-strand	78-83	6	3
β-strand	91-94	4	3

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin	M	protein	99	Homo sapiens	P61769 (AlphaFold model)
T-cell receptor alpha variable 4,TCR alpha chain	A	protein	207	Homo sapiens	A0A0B4J268 (AlphaFold model)
T-cell receptor beta variable 28,TCR beta chain	B	protein	244	Homo sapiens	A0A5B6 (AlphaFold model)
Ala-pro-arg-gly-pro-his-gly-gly-ala-ala-ser-gly-leu	P	protein	13	Homo sapiens	P78358 (AlphaFold model)
HLA class I histocompatibility antigen, B-7 alpha chain	H	protein	362	Homo sapiens	P01889

Sequence of entity 1 (M), FASTA

>6AVF_1 Beta-2-microglobulin (chains M)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 2 (A), FASTA

>6AVF_2 T-cell receptor alpha variable 4,TCR alpha chain (chains A)
MLAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEV
ASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGEILDNFNKFYFGSGTKLNVKPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 3 (B), FASTA

>6AVF_3 T-cell receptor beta variable 28,TCR beta chain (chains B)
MDVKVTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGD
IPEGYSVSREKKERFSLILESASTNQTSMYLCASSQRQEGDTQYFGPGTRLTVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Sequence of entity 4 (P), FASTA

>6AVF_4 ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU (chains P)
APRGPHGGAASGL

Sequence of entity 5 (H), FASTA

>6AVF_5 HLA class I histocompatibility antigen, B-7 alpha chain (chains H)
MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRF
DSDAASPREEPRAPWIEQEGPEYWDRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQ
SMYGCDVGPDGRLLRGHDQYAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQR
RAYLEGECVEWLRRYLENGKDKLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLT
WQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
SSQSTVPIVGIVAGLAVLAVVVIGAVVAAVMCRRKSSGGKGGSYSQAACSDSAQGSDVSL
TA

Primary citation

Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide. Chan, K.F., Gully, B.S., Gras, S. et al. Nat Commun (2018) 9:1026-1026. DOI 10.1038/s41467-018-03321-w · PubMed

Other PDB entries of the same protein (UniProt P61769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4E0K 0.97 Å, Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2…
1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
2YXF 1.13 Å, The high resolution crystal structure of beta2-microglobulin under physiological…
8E2Z 1.13 Å, Structures of HLA-B8E76C loaded with long peptides reveal novel features at the…
7NMR 1.15 Å, Crystal structure of beta-2-microglobulin D76S mutant
8ROP 1.15 Å, Crystal structure of HLA B*18:01 in complex with QEIRTFSF, an 8-mer epitope from…
7R7W 1.17 Å, Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9 S3T variant
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6Y26 1.2 Å, Crystal structure of HLA-B2705 complexed with the nona-peptide mA
7NMC 1.2 Å, Crystal structure of beta-2-microglobulin D76E mutant

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