8TOX: BG505 Env mutant A517E

Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab. Determined by electron microscopy at 2.3 Å resolution. Released 14 Aug 2024.

Method: Electron microscopy
Resolution: 2.3 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 22,008
Mol. weight: 389.08 kDa
Ligands: NAG
Released: 14 Aug 2024

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

Secondary structure: helices and β-sheets

8TOX contains 93 α-helices and 201 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: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	513-515	3	12
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-546	10
α-helix	565-567	3
α-helix	570-595	26
β-strand	603-609	7	13
α-helix	610-611	2
α-helix	619-625	7
α-helix	628-635	8
α-helix	639-662	24

Chains C, G and I: 17 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	13
β-strand	45-47	3	14
β-strand	53-56	4	15
α-helix	58-63	6
β-strand	67	1	16
α-helix	68	1
α-helix	69-73	5
β-strand	75-76	2	15
α-helix	77-78	2
β-strand	83-85	3	14
β-strand	91-94	4	17
α-helix	95-97	3
α-helix	99-116	18
α-helix	120	1
β-strand	121	1	18
β-strand	129-133	5	19
β-strand	138	1	20
α-helix	140-150	3
β-strand	154-162	9	19
β-strand	169-177	9	19
α-helix	178-180	3
β-strand	181-183	3	19
β-strand	190-193	4	19
α-helix	194-197	4
α-helix	200-201	2
β-strand	202-203	2	18
α-helix	204-205	2
β-strand	209	1	16
β-strand	215	1	21
β-strand	216-218	3	15
β-strand	223-228	6	14
β-strand	236-239	4	17
β-strand	242-245	4	14
β-strand	247	1	15
β-strand	251	1	21
β-strand	260-261	2	19
β-strand	271-273	3	19
β-strand	284-312	27	19
β-strand	315-323	10	19
β-strand	326	1	20
β-strand	330-333	4	19
α-helix	335-353	19
β-strand	358-361	4	19
α-helix	369-372	4
β-strand	374-378	5	22
β-strand	381-385	5	22
β-strand	393-395	3	19
β-strand	414-417	4	19
β-strand	418-421	4	22
β-strand	423-424	2	18
β-strand	434-435	2	18
α-helix	437-439	3
β-strand	441-456	16	19
α-helix	459-461	3
β-strand	465-470	6	19
α-helix	476-483	8
β-strand	486-491	6	14
β-strand	494-499	6	13

Chains D, H and J: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	39
β-strand	11-12	2	40
β-strand	17-25	9	39
α-helix	29-31	3
β-strand	34-39	6	41
β-strand	45-51	7	41
β-strand	57-59	3	41
β-strand	69-72	4	39
β-strand	77-82A	7	39
α-helix	84-86	3
β-strand	88-94	7	41
β-strand	100-100C	4	12
β-strand	100F-100J	5	12
β-strand	102-103	2	41
β-strand	107-109	3	41
β-strand	110-111	2	40

Chains E, K and L: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	42
β-strand	10-13	4	43
β-strand	19-25	7	42
β-strand	33-38	6	43
β-strand	44-49	6	43
β-strand	53-54	2	43
α-helix	55	1
β-strand	62-67	6	42
β-strand	70-75	6	42
α-helix	80-82	3
β-strand	85-90	6	43
α-helix	97-99	3
β-strand	102-106	5	43

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp41	A, B, F	protein	153	Human immunodeficiency virus 1	Q2N0S6
Envelope glycoprotein gp120	C, G, I	protein	475	Human immunodeficiency virus 1	Q2N0S6
antibody ACS202 Fab heavy chain	D, H, J	protein	236	Homo sapiens
antibody ACS202 Fab light chain	E, K, L	protein	214	Homo sapiens

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

>8TOX_1 Envelope glycoprotein gp41 (chains A, B, F)
AVGIGEVFLGFLGAAGSTMGAASNTLTVQARQLLSGIVQQQSNLLRAPEAQQHLLKLGVW
GFKQLQARVLAVERYLEVQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEIGNYTQIIYGLLEESQFQQEINEQDLLALD

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

>8TOX_2 Envelope glycoprotein gp120 (chains C, G, I)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQICPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCKNVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNIIVQFNTPVQINCTRPNNMTRKSIRIGPGQAFYALGDIIGDIRQPHC
TVSKATWNETLGKVVKQLRKHFGNNTIIFFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRVGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVG

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

>8TOX_3 antibody ACS202 Fab heavy chain (chains D, H, J)
QVQLVESGGGVVQPGGSLRLSCAASGFAFKDFGMHWVRQAPGKGLEWVAVIGGGHGQHQS
YSESVKGRFAITRDNEKNKLYLHMDRLRTEDTAVYYCAKDRLGRPWNIGGRLVYYYYGMD
VWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

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

>8TOX_4 antibody ACS202 Fab light chain (chains E, K, L)
AIRMTQSPSSLSASVGDRVTITCQASQDIKKSLNWYRQKPGKAPELLIHDASILQTGVPS
AFTASGSGTHFSFVINKLQPEDVGTYFCQEYENLQFTFGPGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide. Reveiz, M., Xu, K., Lee, M. et al. Front Immunol (2024) 15:1484029-1484029. DOI 10.3389/fimmu.2024.1484029 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S6), best resolution first:

6MTJ 2.34 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6W03 2.4 Å, Crystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with…
6MTN 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6UDJ 2.5 Å, HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074
8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6MU7 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6MU6 2.55 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6NNJ 2.6 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in…
8EUV 2.6 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB
8T4K 2.6 Å, MD64 N332-GT5 sosip
8EUU 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB
8EUW 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-MM28 FAB

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