8GVI: The complex between H25-11 TCR and HLA-A24

The complex between H25-11 TCR and HLA-A24 bound to HIV-1 Nef138-8 peptide. Determined by X-ray diffraction at 3.3 Å resolution. Released 19 Oct 2022.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Homo sapiens, HIV whole-genome vector AA1305#18
Chains: 5
Atoms: 6,666
Mol. weight: 96.05 kDa
Released: 19 Oct 2022

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

Secondary structure: helices and β-sheets

8GVI contains 23 α-helices and 81 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: 5 helices, 22 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
α-helix	61-63	3
β-strand	65-69	5	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	89-95	7	2
β-strand	103-105	3	2
β-strand	109-114	6	2
β-strand	123-126	4	3
β-strand	128	1	4
α-helix	129-130	2
β-strand	136-141	6	3
β-strand	148	1	5
β-strand	158-159	2	3
β-strand	165-167	3	6
β-strand	172-174	3	6
β-strand	176-181	6	3
α-helix	188-190	3
α-helix	192-194	3
β-strand	196	1	5
β-strand	202	1	3

Chain B: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	7
β-strand	11	1	8
β-strand	14-15	2	9
β-strand	20-25	6	7
β-strand	32-38	7	8
α-helix	43	1
β-strand	44-51	8	8
β-strand	54-58	5	8
β-strand	66-69	4	7
β-strand	76-80	5	7
α-helix	85-87	3
β-strand	90-96	7	8
β-strand	106-107	2	8
β-strand	111-112	2	8
β-strand	115-116	2	9
β-strand	123	1	10
α-helix	124-125	2
β-strand	126-130	5	11
β-strand	131	1	4
α-helix	132-133	2
α-helix	134-140	7
β-strand	142-152	11	11
β-strand	153	1	10
β-strand	157-163	7	12
β-strand	166-167	2	12
β-strand	172-174	3	11
β-strand	179-180	2	11
β-strand	190-199	10	11
α-helix	200-202	3
β-strand	209-216	8	12
β-strand	219	1	13
β-strand	233	1	13
β-strand	235-242	8	12

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	14
β-strand	5-12	8	15
β-strand	21-28	8	15
β-strand	31-37	7	15
β-strand	46-47	2	15
α-helix	51-54	4
α-helix	57-85	29
β-strand	94-98	5	15
β-strand	101-103	3	14
β-strand	109-112	4	14
β-strand	115-118	4	15
β-strand	121-125	5	15
β-strand	126	1	16
β-strand	133	1	16
α-helix	138-144	7
α-helix	146-149	4
α-helix	153-158	6
α-helix	159-164	6
α-helix	165-174	10
α-helix	183-185	3
β-strand	186-193	8	17
β-strand	198-208	11	17
β-strand	214-219	6	18
β-strand	223	1	18
β-strand	230	1	17
α-helix	231-233	3
β-strand	234-235	2	17
β-strand	241-250	10	17
β-strand	257-262	6	18
β-strand	270-272	3	18

Chain L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	19
α-helix	4-5	2
β-strand	6-11	6	20
β-strand	21-30	10	20
β-strand	31	1	19
β-strand	35-41	7	21
β-strand	44-45	2	21
α-helix	46	1
β-strand	50-51	2	20
β-strand	55-56	2	20
β-strand	62-70	9	20
β-strand	78-84	7	21
β-strand	91-94	4	21

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H25-11 TCR alpha chain	A	protein	209	Homo sapiens
H25-11 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 whole-genome vector AA1305#18	P04601 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8GVI_1 H25-11 TCR alpha chain (chains A)
MAQSVTQPDIHITVSEGASLELRCNYSYGATPYLFWYVQSPGQGLQLLLKYFSGDTLVQG
IKGFEAEFKRSQSSFNLRKPSVHWSDAAEYFCAVVFTGGGNKLTFGTGTQLKVELNIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>8GVI_2 H25-11 TCR beta chain (chains B)
MDTGVSQDPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSR
LLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSLRDRVPETQYFGPGTRLLVLEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Sequence of entity 3 (H), FASTA

>8GVI_3 MHC class I antigen (chains H)
MGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETL
QRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 4 (L), FASTA

>8GVI_4 Beta-2-microglobulin (chains L)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (P), FASTA

>8GVI_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:

8GVB 3.2 Å, The complex between public TCR TD08 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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