8FR6: Antibody vFP53.02

Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP. Determined by electron microscopy at 2.5 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Human immunodeficiency virus 1, Mus musculus
Chains: 12
Atoms: 21,237
Mol. weight: 387.71 kDa
Ligands: NAG
Released: 19 Apr 2023

Explore 8FR6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FR6 contains 82 α-helices and 210 β-strands across 12 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, B and F: 10 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	516-519	4
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-543	7
α-helix	570-595	26
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	619-624	6
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-660	22

Chain C: 15 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	3
β-strand	53-56	4	4
α-helix	58-61	4
β-strand	67	1	5
β-strand	75-76	2	4
α-helix	77-78	2
β-strand	83-86	4	3
β-strand	91-94	4	6
α-helix	102-114	13
β-strand	121-122	2	7
β-strand	129-133	5	8
β-strand	138	1	9
α-helix	140-150	3
β-strand	154-162	9	8
β-strand	169-177	9	8
α-helix	178-180	3
β-strand	181-184	4	8
β-strand	190-193	4	8
α-helix	194-197	4
α-helix	200	1
β-strand	201-203	3	7
α-helix	204-205	2
β-strand	209	1	5
β-strand	215	1	10
β-strand	216-218	3	4
β-strand	223-228	6	3
β-strand	236-239	4	6
β-strand	242-245	4	3
β-strand	247	1	4
β-strand	251	1	10
β-strand	260-261	2	11
β-strand	271-273	3	11
α-helix	283	1
β-strand	284-300	17	11
β-strand	301	1	12
β-strand	302	1	11
β-strand	304-312	7	13
β-strand	315-320	6	13
β-strand	323	1	12
β-strand	326	1	9
β-strand	329-334	6	11
α-helix	335-353	19
β-strand	358-361	4	11
α-helix	369-372	4
β-strand	374-378	5	11
β-strand	381-385	5	11
α-helix	387-389	3
β-strand	393-395	3	11
β-strand	413-421	9	11
β-strand	423-424	2	7
α-helix	426-428	3
β-strand	434-435	2	7
α-helix	436-438	3
β-strand	441-456	16	11
β-strand	465-470	6	11
α-helix	476-483	8
β-strand	486-491	6	3
β-strand	494-499	6	1

Chains D, H and J: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	37
β-strand	9-12	4	38
β-strand	18-19	2	37
β-strand	22-25	4	37
β-strand	33-39	7	38
β-strand	46-51	6	38
β-strand	57-59	3	38
β-strand	68-72	5	37
β-strand	77-82	6	37
α-helix	84-86	3
β-strand	89-95	7	38
β-strand	104	1	37
β-strand	108-111	4	38

Chains E, K and L: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	39
β-strand	10-14	5	38
β-strand	19-25	7	39
β-strand	27C	1	40
β-strand	31	1	40
β-strand	33-38	6	38
β-strand	45-49	5	38
β-strand	53-54	2	38
β-strand	62-67	6	39
β-strand	70-75	6	39
α-helix	80-82	3
β-strand	84-90	7	38
α-helix	96	1
β-strand	97-98	2	38
β-strand	102-107	6	38

Chains G and I: 14 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	2
β-strand	45-47	3	15
β-strand	53-56	4	16
α-helix	58-61	4
β-strand	67	1	17
β-strand	75-76	2	16
α-helix	77-78	2
β-strand	83-86	4	15
β-strand	91-94	4	18
α-helix	102-114	13
β-strand	121-122	2	19
β-strand	129-133	5	20
β-strand	138	1	21
α-helix	140-150	3
β-strand	154-162	9	20
β-strand	169-177	9	20
β-strand	181-184	4	20
β-strand	190-193	4	20
α-helix	194-197	4
α-helix	200	1
β-strand	201-203	3	19
α-helix	204-205	2
β-strand	209	1	17
β-strand	215	1	22
β-strand	216-218	3	16
β-strand	223-228	6	15
β-strand	236-239	4	18
β-strand	242-245	4	15
β-strand	247	1	16
β-strand	251	1	22
β-strand	260-261	2	23
β-strand	271-273	3	23
α-helix	283	1
β-strand	284-300	17	23
β-strand	301	1	24
β-strand	302	1	23
β-strand	304-312	7	25
β-strand	315-320	6	25
β-strand	323	1	24
β-strand	326	1	21
β-strand	329-334	6	23
α-helix	335-353	19
β-strand	358-361	4	23
α-helix	369-372	4
β-strand	374-378	5	23
β-strand	381-385	5	23
α-helix	387-389	3
β-strand	393-395	3	23
β-strand	413-421	9	23
β-strand	423-424	2	19
α-helix	426-428	3
β-strand	434-435	2	19
α-helix	436-438	3
β-strand	441-456	16	23
β-strand	465-470	6	23
α-helix	476-483	8
β-strand	486-491	6	15
β-strand	494-499	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp41	A, B, F	protein	153	Human immunodeficiency virus 1	Q2N0S7
Envelope glycoprotein gp120	C, G, I	protein	473	Human immunodeficiency virus 1	Q2N0S6
vFP53.02 Fab heavy chain	D, H, J	protein	230	Mus musculus
vFP53.02 Fab light chain	E, K, L	protein	219	Mus musculus

Sequence of entity 1 (A, B, F), FASTA

>8FR6_1 Envelope glycoprotein gp41 (chains A, B, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (C, G, I), FASTA

>8FR6_2 Envelope glycoprotein gp120 (chains C, G, I)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

Sequence of entity 3 (D, H, J), FASTA

>8FR6_3 vFP53.02 Fab heavy chain (chains D, H, J)
QAQLQQSGTELVRPGASVTLSCKASGYKFNDYEIHWVKQTPVHGLEWIGAIVPETGFTAY
SQKFRGKALLTADKSSSTVYMDLRSLTSADSAVFYCSRLQLFGYFDVWGTGTTVIVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 4 (E, K, L), FASTA

>8FR6_4 vFP53.02 Fab light chain (chains E, K, L)
DVLMTQNPLSLPVSLGDQASISCRSSQSVVYSDGNAYLEWYLQKPGQSPKLLIYKASNRF
SGVPDRFSASGSGTDFTLRISRVETEDLGLYYCFQGTHIPYTFGGGTKLEMKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	21

Primary citation

Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization. Sastry, M., Changela, A., Gorman, J. et al. J Virol (2023) 97:e0160422-e0160422. DOI 10.1128/jvi.01604-22 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S7), best resolution first:

5I8C 1.54 Å, Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex…
6WX2 2.39 Å, Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with F60P mutation on…
8G4T 2.81 Å, Vaccine-elicited human antibody 2C09 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
8G4M 2.95 Å, Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6MPG 3.2 Å, Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody,…
6UM7 3.5 Å, Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex…
9PNN 3.5 Å, Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
6CM3 3.54 Å, BG505 SOSIP in complex with sCD4, 17b, 8ANC195
6CDI 3.6 Å, Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex…
8DOW 3.69 Å, Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
7LL1 3.73 Å, Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly…

Browse structure collections

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