8GVB: The complex between public TCR TD08 and HLA-A24

The complex between public TCR TD08 and HLA-A24 bound to HIV-1 Nef138-8 peptide. Determined by X-ray diffraction at 3.2 Å resolution. Released 19 Oct 2022.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, HIV-1 06TG.HT008
Chains: 5
Atoms: 6,462
Mol. weight: 96.01 kDa
Released: 19 Oct 2022

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

Secondary structure: helices and β-sheets

8GVB contains 20 α-helices and 74 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: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
β-strand	11-15	5	2
β-strand	20-22	3	1
β-strand	25	1	1
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	57-59	3	1
β-strand	65-69	5	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	89-95	7	2
α-helix	97-99	3
β-strand	103-105	3	2
β-strand	109-114	6	2
β-strand	123-127	5	3
β-strand	128	1	4
α-helix	129-130	2
β-strand	137-141	5	3
α-helix	160-162	3
β-strand	163-167	5	5
β-strand	172-176	5	5
β-strand	178	1	3

Chain B: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	6
β-strand	11-15	5	7
β-strand	20-25	6	6
β-strand	33-38	6	7
β-strand	44-50	7	7
β-strand	55-58	4	7
β-strand	66-69	4	6
β-strand	76-80	5	6
α-helix	85-87	3
β-strand	90-95	6	7
β-strand	106-107	2	7
β-strand	111-116	6	7
β-strand	123	1	8
β-strand	126-130	5	9
β-strand	131	1	4
α-helix	132-133	2
α-helix	134-140	7
β-strand	142-152	11	9
β-strand	153	1	8
β-strand	157-163	7	10
β-strand	166-167	2	10
β-strand	172-174	3	9
β-strand	179-180	2	9
β-strand	190-199	10	9
α-helix	200-203	4
β-strand	209-216	8	10
β-strand	235-242	8	10

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
α-helix	20	1
β-strand	21-28	8	11
β-strand	31-37	7	11
β-strand	46-47	2	11
α-helix	51-54	4
α-helix	57-85	29
β-strand	94-98	5	11
β-strand	101-103	3	11
β-strand	109-112	4	11
β-strand	115-118	4	11
β-strand	121-126	6	11
β-strand	133-135	3	11
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
β-strand	183	1	12
α-helix	184-185	2
β-strand	186-189	4	13
β-strand	192-193	2	13
β-strand	198-208	11	13
β-strand	209	1	12
β-strand	213-219	7	14
β-strand	222-223	2	14
β-strand	228-230	3	13
α-helix	231-233	3
β-strand	234-235	2	13
β-strand	241-250	10	13
α-helix	254-256	3
β-strand	257-263	7	14
β-strand	270-273	4	14

Chain L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
β-strand	6-11	6	16
β-strand	21-30	10	16
β-strand	31	1	15
β-strand	36-41	6	17
β-strand	44-45	2	17
β-strand	50-51	2	16
α-helix	52-54	3
β-strand	55-56	2	16
β-strand	62-70	9	16
β-strand	78-83	6	17
β-strand	91-94	4	17
α-helix	95-96	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TD08 TCR alpha chain	A	protein	209	Homo sapiens
TD08 TCR beta chain	B	protein	246	Homo sapiens
MHC class I antigen	H	protein	275	Homo sapiens	F6IQZ4 (AlphaFold model)
Beta-2-microglobulin	L	protein	100	Homo sapiens	P61769 (AlphaFold model)
8-mer peptide from Protein Nef	P	protein	8	HIV-1 06TG.HT008	P04601 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8GVB_1 TD08 TCR alpha chain (chains A)
MAQSVTQPDIHITVSEGASLELRCNYSYGATPYLFWYVQSPGQGLQLLLKYFSGDTLVQG
IKGFEAEFKRSQSSFNLRKPSVHWSDAAEYFCAVGFTGGGNKLTFGTGTQLKVELNIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>8GVB_2 TD08 TCR beta chain (chains B)
MDTGVSQDPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSR
LLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSDRDRVPETQYFGPGTRLLVLEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Sequence of entity 3 (H), FASTA

>8GVB_3 MHC class I antigen (chains H)
MGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETL
QRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 4 (L), FASTA

>8GVB_4 Beta-2-microglobulin (chains L)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (P), FASTA

>8GVB_5 8-mer peptide from Protein Nef (chains P)
RYPLTFGW

Primary citation

Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors. Ma, K., Chai, Y., Guan, J. et al. J Immunol (2022) 209:1652-1661. DOI 10.4049/jimmunol.2200191 · PubMed

Other PDB entries of the same protein (UniProt F6IQZ4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GVI 3.3 Å, The complex between H25-11 TCR and HLA-A24 bound to HIV-1 Nef138-8 peptide
8GVG 3.37 Å, The complex between public TCR TD08 and HLA-A24 bound to HIV-1 Nef138-8 (2F) peptide

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