8G8D: DH1346 Fab

Crystal structure of DH1346 Fab in complex with HIV proximal MPER peptide. Determined by X-ray diffraction at 2.02 Å resolution. Released 22 May 2024.

Method: X-ray diffraction
Resolution: 2.02 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 6
Atoms: 7,572
Mol. weight: 104.86 kDa
Ligands: F
Released: 22 May 2024

Explore 8G8D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G8D contains 43 α-helices and 89 β-strands across 6 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: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	57-59	3	12
α-helix	60	1
β-strand	67-72	6	11
α-helix	73-75	3
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-99	12	12
β-strand	100F-103	8	12
β-strand	107-111	5	12
α-helix	115-116	2
β-strand	117	1	13
α-helix	118-119	2
β-strand	120-124	5	14
α-helix	128-130	3
β-strand	131	1	14
β-strand	135-145	11	14
β-strand	146	1	13
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	169-170	2	14
β-strand	176-185	10	14
α-helix	186-190	5
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5
α-helix	213-215	3

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	15
β-strand	9-14	5	16
β-strand	19-24	6	15
α-helix	26-29	4
β-strand	34-38	5	16
α-helix	43-44	2
β-strand	45-48	4	16
β-strand	49	1	17
β-strand	53	1	17
β-strand	62-67	6	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	85-91	7	16
β-strand	96-98	3	16
β-strand	102-106A	6	16
α-helix	108-110	3
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-155	3	20
β-strand	159-161	3	19
α-helix	162-164	3
β-strand	165-166	2	19
β-strand	172-180	9	19
α-helix	182-187	6
β-strand	191-197	7	20
β-strand	200-206	7	20

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	659-682	24

Chain H: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	57-59	3	2
α-helix	60	1
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-99	12	2
β-strand	100F-103	8	2
β-strand	107-111	5	2
α-helix	115-116	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	128-130	3
β-strand	131-132	2	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-190	5
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	6
β-strand	9-14	5	7
β-strand	19-24	6	6
α-helix	26-29	4
β-strand	34-38	5	7
α-helix	43-44	2
β-strand	45-48	4	7
β-strand	49	1	8
β-strand	53	1	8
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-91	7	7
β-strand	96-98	3	7
β-strand	102-106A	6	7
α-helix	108-110	3
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	9
β-strand	145-150	6	10
β-strand	153-155	3	10
β-strand	159-161	3	9
β-strand	165-166	2	9
β-strand	172-180	9	9
α-helix	182-185	4
β-strand	191-197	7	10
β-strand	200-206	7	10

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	658-682	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DH1346 heavy chain	A, H	protein	230	Homo sapiens	P0DOX5 (AlphaFold model)
DH1346 light chain	B, L	protein	215	Homo sapiens
gp41 MPER peptide	C, P	protein	34	Human immunodeficiency virus 1	P04578 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>8G8D_1 DH1346 heavy chain (chains A, H)
QVQLVQSGSELKKPGASVKVSCKASGYTFNNYAMNWVRQAPGQGLEWMGWINTNTGNPTY
GQGFTGRFVFSLDTSVSTAYLQISSLKTEDTAVYYCARFRVAPAAQRGYFYYYMDVWGKG
TTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B, L), FASTA

>8G8D_2 DH1346 light chain (chains B, L)
SSELTQDPTVSVALGQTVTITCQGDSLRWYSASWYQQKPGQTPVLLIYNKDNRPSGIPDR
FSGSSSENTASLTITGAQAEDEADYYCHSRDNNVFPNWVFGGGTKLTVLGQPKAAPSVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (C, P), FASTA

>8G8D_3 gp41 MPER peptide (chains C, P)
KKKNEQELLELDKWASLWNWFDITNWLWYIRKKK

Ligands and cofactors

ID	Name	Formula	Copies
F	Fluoride ion	F	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans. Williams, W.B., Alam, S.M., Ofek, G. et al. Cell (2024) 187:2919-2934.e20. DOI 10.1016/j.cell.2024.04.033 · PubMed

Other PDB entries of the same protein (UniProt P0DOX5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
6YTB 1.65 Å, Glycosylated knob/dummy-hole/dummy fc fragment
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
8ECV 1.81 Å, Bovine Fab 2F12
6G1E 1.88 Å, BEAT Fc with improved heterodimerization (Q3A-D84.4Q)
5W5L 1.9 Å, Crystal structure of human IgG1-Sigma Fc fragment
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
6DKJ 1.95 Å, human GIPR ECD and Fab complex
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6UGW 2.0 Å, Crystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a…

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