6AVG: KFJ37 TCR-NY-ESO-1-HLA-B*07:02 complex

Crystal structure of the KFJ37 TCR-NY-ESO-1-HLA-B*07:02 complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 28 Feb 2018.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,701
Mol. weight: 208.52 kDa
Released: 28 Feb 2018

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

Secondary structure: helices and β-sheets

6AVG contains 42 α-helices and 140 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.

Chains A and H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	17
α-helix	4-5	2
β-strand	6-11	6	18
β-strand	21-30	10	18
β-strand	31	1	17
β-strand	36-41	6	19
β-strand	44-45	2	19
β-strand	50-51	2	18
β-strand	55-56	2	18
β-strand	62-70	9	18
β-strand	78-83	6	19
α-helix	90	1
β-strand	91-94	4	19

Chain B: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	20
β-strand	12-16	5	21
β-strand	21-26	6	20
β-strand	35-41	7	21
β-strand	48-53	6	21
β-strand	58-59	2	20
β-strand	64-66	3	20
β-strand	73-78	6	20
α-helix	83-85	3
β-strand	87-94	8	21
β-strand	104-109	6	21
β-strand	118-122	5	22
β-strand	131-136	6	22
β-strand	152-154	3	22
α-helix	155-157	3
β-strand	158-162	5	22
α-helix	163-165	3
β-strand	167-176	10	22
α-helix	183-185	3
β-strand	197	1	22

Chain C: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	4
β-strand	12-16	5	5
β-strand	21-26	6	4
β-strand	35-41	7	5
β-strand	48-53	6	5
β-strand	58-59	2	4
β-strand	64-66	3	4
β-strand	73-78	6	4
α-helix	83-85	3
β-strand	87-94	8	5
β-strand	104-109	6	5
β-strand	118-122	5	6
β-strand	131-136	6	6
β-strand	153-154	2	6
α-helix	155-157	3
β-strand	158-162	5	6
α-helix	163-165	3
β-strand	167-176	10	6
α-helix	183-185	3
β-strand	197	1	6

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	7
β-strand	13-17	5	8
β-strand	22-27	6	7
β-strand	34-40	7	8
β-strand	47-53	7	8
β-strand	56-60	5	8
β-strand	67-71	5	7
β-strand	77-81	5	7
α-helix	86-88	3
β-strand	90-97	8	8
β-strand	107-108	2	8
β-strand	112-117	6	8
β-strand	124	1	9
β-strand	127-131	5	10
α-helix	132-134	3
α-helix	135-141	7
β-strand	143-153	11	10
β-strand	154	1	9
β-strand	158-164	7	11
β-strand	167-169	3	11
β-strand	173-175	3	10
α-helix	179	1
β-strand	180-181	2	10
β-strand	191-200	10	10
α-helix	201-205	5
β-strand	210-217	8	11
β-strand	220	1	12
α-helix	231-232	2
β-strand	234	1	12
β-strand	236-243	8	11

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	23
β-strand	13-17	5	24
β-strand	22-27	6	23
β-strand	34-40	7	24
β-strand	47-53	7	24
β-strand	56-60	5	24
β-strand	67-71	5	23
β-strand	77-81	5	23
α-helix	86-88	3
β-strand	90-97	8	24
β-strand	107-108	2	24
β-strand	112-117	6	24
β-strand	124	1	25
β-strand	127-131	5	26
α-helix	132-134	3
α-helix	135-141	7
β-strand	143-153	11	26
β-strand	154	1	25
β-strand	158-164	7	27
β-strand	167-169	3	27
β-strand	173-175	3	26
α-helix	179	1
β-strand	180-181	2	26
β-strand	191-200	10	26
α-helix	201-205	5
β-strand	210-217	8	27
β-strand	220	1	28
β-strand	234	1	28
β-strand	236-243	8	27

Chain F: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	29
β-strand	21-28	8	29
β-strand	31-37	7	29
β-strand	46-47	2	29
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	29
β-strand	109-118	10	29
β-strand	121-126	6	29
β-strand	133-135	3	29
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	30
α-helix	184-185	2
β-strand	186-193	8	31
β-strand	198-208	11	31
β-strand	209	1	30
β-strand	214-219	6	32
β-strand	222-223	2	32
β-strand	228-230	3	31
α-helix	231-233	3
β-strand	234-235	2	31
β-strand	241-250	10	31
α-helix	254-256	3
β-strand	257-262	6	32
β-strand	270-272	3	32

Chain G: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	13
α-helix	20	1
β-strand	21-28	8	13
β-strand	31-37	7	13
β-strand	46-47	2	13
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	13
β-strand	109-118	10	13
β-strand	121-126	6	13
β-strand	133-135	3	13
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	14
α-helix	184-185	2
β-strand	186-193	8	15
β-strand	199-208	10	15
β-strand	209	1	14
β-strand	214-219	6	16
β-strand	222-223	2	16
β-strand	228-230	3	15
α-helix	231-233	3
β-strand	234-235	2	15
β-strand	241-249	9	15
α-helix	254-256	3
β-strand	257-262	6	16
β-strand	270-272	3	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin	A, H	protein	107	Homo sapiens	P61769 (AlphaFold model)
T-cell receptor alpha variable 4,TCR alpha chain	B, C	protein	202	Homo sapiens	A0A0B4J268 (AlphaFold model)
T-cell receptor beta variable 9,TCR beta chain	D, E	protein	245	Homo sapiens	A0A0B4J1U6 (AlphaFold model)
HLA class I histocompatibility antigen, B-7 alpha chain	F, G	protein	362	Homo sapiens	P01889 (AlphaFold model)
Ala-pro-arg-gly-pro-his-gly-gly-ala-ala-ser-gly-leu	P, Q	protein	13	Homo sapiens	P78358

Sequence of entity 1 (A, H), FASTA

>6AVG_1 Beta-2-microglobulin (chains A, H)
LSLSGLEAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHS
DLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 2 (B, C), FASTA

>6AVG_2 T-cell receptor alpha variable 4,TCR alpha chain (chains B, C)
MLAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEV
ASLFIPADRKSSTLSLPRVSLSDTAVYYCLVVDQKLVFGTGTRLLVSPNIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTFFPSPESS

Sequence of entity 3 (D, E), FASTA

>6AVG_3 T-cell receptor beta variable 9,TCR beta chain (chains D, E)
MDSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGN
ILERFSAQQFPDLHSELNLSSLELGDSALYFCASSGGHTGSNEQFFGPGTRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Sequence of entity 4 (F, G), FASTA

>6AVG_4 HLA class I histocompatibility antigen, B-7 alpha chain (chains F, G)
MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRF
DSDAASPREEPRAPWIEQEGPEYWDRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQ
SMYGCDVGPDGRLLRGHDQYAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQR
RAYLEGECVEWLRRYLENGKDKLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLT
WQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
SSQSTVPIVGIVAGLAVLAVVVIGAVVAAVMCRRKSSGGKGGSYSQAACSDSAQGSDVSL
TA

Sequence of entity 5 (P, Q), FASTA

>6AVG_5 ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU (chains P, Q)
APRGPHGGAASGL

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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