8TQ7: Fab.34.2.12

Crystal structure of Fab.34.2.12 in complex with MHC-I (H2-Dd). Determined by X-ray diffraction at 2.8 Å resolution. Released 20 Mar 2024.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Mus musculus, HIV-1 M:B_HXB2R
Chains: 10
Atoms: 12,530
Mol. weight: 182.2 kDa
Released: 20 Mar 2024

Explore 8TQ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TQ7 contains 49 α-helices and 144 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.

Chain A: 11 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	52-54	3
α-helix	57-84	28
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
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	3	1	5
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
α-helix	90	1
β-strand	91-94	4	7

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	8
β-strand	18-28	11	8
β-strand	31-37	7	8
β-strand	45-47	3	8
α-helix	52-54	3
α-helix	57-85	29
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
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	9
β-strand	188-193	6	10
β-strand	198-206	9	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
α-helix	225-227	3
β-strand	229-230	2	10
α-helix	232-233	2
β-strand	234	1	10
β-strand	242-250	9	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-273	4	11

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	35-41	7	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-84	7	14
β-strand	91-94	4	14

Chain F: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
β-strand	10-12	3	16
β-strand	18-25	8	15
β-strand	33-39	7	16
β-strand	45-52	8	16
β-strand	57-60	4	16
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-99	8	16
β-strand	106-107	2	16
β-strand	111-115	5	16
α-helix	118-120	3
β-strand	121	1	17
β-strand	124-128	5	18
β-strand	139-149	11	18
β-strand	150	1	17
β-strand	155-158	4	19
β-strand	167-175	9	18
β-strand	178-188	11	18
β-strand	198-203	6	19
α-helix	204-206	3
β-strand	208-213	6	19

Chain G: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	20
β-strand	10-14	5	16
β-strand	19-24	6	21
β-strand	25	1	20
β-strand	33-38	6	16
β-strand	45-49	5	16
β-strand	53-54	2	16
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	85-90	6	16
α-helix	96	1
β-strand	97-98	2	16
β-strand	102-107	6	16
β-strand	111	1	22
α-helix	112-113	2
β-strand	114-118	5	23
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	23
β-strand	140	1	22
β-strand	144-150	7	24
β-strand	153-155	3	24
β-strand	159-163	5	23
α-helix	164-167	4
β-strand	173-182	10	23
α-helix	183-188	6
β-strand	191-198	8	24
β-strand	205-210	6	24

Chain H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	25
α-helix	7-9	3
β-strand	10-12	3	26
β-strand	18-25	8	25
β-strand	33-39	7	26
β-strand	45-52	8	26
β-strand	57-60	4	26
α-helix	62-64	3
β-strand	68-73	6	25
β-strand	78-83	6	25
α-helix	88-90	3
β-strand	92-99	8	26
β-strand	101	1	27
β-strand	103	1	27
β-strand	106-107	2	26
β-strand	111-115	5	26
α-helix	119-120	2
β-strand	121	1	28
β-strand	124-128	5	29
β-strand	141-149	9	29
β-strand	150	1	28
β-strand	155-158	4	30
β-strand	167-169	3	29
α-helix	170-172	3
β-strand	173-175	3	29
β-strand	178-186	9	29
β-strand	198-203	6	30
β-strand	208-213	6	30

Chain L: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	31
β-strand	10-12	3	32
β-strand	19-25	7	31
β-strand	33-38	6	32
β-strand	45-49	5	32
β-strand	53-54	2	32
α-helix	55	1
β-strand	62-67	6	31
β-strand	70-75	6	31
α-helix	80-82	3
β-strand	85-90	6	32
α-helix	96	1
β-strand	97-98	2	32
β-strand	102-105	4	32
β-strand	114-118	5	33
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	33
β-strand	145-150	6	34
β-strand	153-155	3	34
β-strand	159-163	5	33
α-helix	164-167	4
β-strand	173-182	10	33
α-helix	183-187	5
β-strand	191-197	7	34
β-strand	205-210	6	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A, C	protein	273	Mus musculus	P01900 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Mus musculus	P01887 (AlphaFold model)
Transmembrane protein gp41	E, P	protein	10	HIV-1 M:B_HXB2R	P04578 (AlphaFold model)
Fab.34.2.12 Heavy Chain	F, H	protein	215	Mus musculus
Fab 34.2.12 Light Chain	G, L	protein	213	Mus musculus

Sequence of entity 1 (A, C), FASTA

>8TQ7_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A, C)
SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWE
RETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGC
DYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLR
TDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTF
QKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRW

Sequence of entity 2 (B, D), FASTA

>8TQ7_2 Beta-2-microglobulin (chains B, D)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (E, P), FASTA

>8TQ7_3 Transmembrane protein gp41 (chains E, P)
RGPGRAFVTI

Sequence of entity 4 (F, H), FASTA

>8TQ7_4 Fab.34.2.12 Heavy Chain (chains F, H)
QVQLQQSGPELVKPGASVKISCQSSGYTISNSWMNWVKQRPGKGLEWIGRIYPGDGDTHY
NGKFKAKATLTADRSSSTAYMHLSSLTSEDSAIYFCARSTAAWFPYWGRGTLVTVSAAKT
TAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIE

Sequence of entity 5 (G, L), FASTA

>8TQ7_5 Fab 34.2.12 Light Chain (chains G, L)
TTVTQTPKFMSTSVGDRVSVTCTASQNVDTNVAWYQQKPGQSPKPLIFSASSRYTGIPDR
FGGSGSGTDFALTISNVQSEDLAEYFCQQYHSFPYTFGGGTRLEIKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction. Boyd, L.F., Jiang, J., Ahmad, J. et al. J Immunol (2024) 212:1366-1380. DOI 10.4049/jimmunol.2300839 · PubMed

Other PDB entries of the same protein (UniProt P01900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…
8FHU 1.8 Å, Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by…
5T7G 1.96 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
3E6H 2.1 Å, MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…
5IVX 2.1 Å, Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex
8FHL 2.19 Å, Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented…
1QO3 2.3 Å, Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
8D5F 2.31 Å, The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
5KD7 2.35 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
6NPR 2.37 Å, Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide…
1BII 2.4 Å, The crystal structure of H-2DD MHC class I in complex with the HIV-1 derived peptide…

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