8EUV: HIV-1 BG505 DS-SOSIP ENV trimer

Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB. Determined by electron microscopy at 2.6 Å resolution. Released 27 Sept 2023.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,138
Mol. weight: 372.64 kDa
Ligands: NAG
Released: 27 Sept 2023

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

Secondary structure: helices and β-sheets

8EUV contains 61 α-helices and 195 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.

Chain A: 8 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	1
β-strand	45-47	3	2
β-strand	53-56	4	3
β-strand	67	1	4
β-strand	75-76	2	3
α-helix	77-78	2
β-strand	83-86	4	2
β-strand	91-94	4	5
α-helix	99-115	17
β-strand	121	1	6
β-strand	129-133	5	7
β-strand	138	1	8
β-strand	154-162	9	7
β-strand	169-177	9	7
β-strand	181-183	3	7
β-strand	190-193	4	7
β-strand	201-203	3	6
α-helix	204-205	2
β-strand	209	1	4
β-strand	215	1	9
β-strand	216-218	3	3
β-strand	223-228	6	2
β-strand	236-239	4	5
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	9
β-strand	259-261	3	10
β-strand	271-273	3	10
α-helix	283	1
β-strand	284-298	15	10
β-strand	304-312	7	11
β-strand	315-320	6	11
β-strand	326	1	8
β-strand	329-334	6	10
α-helix	335-353	19
β-strand	358-361	4	10
α-helix	369-372	4
β-strand	374-378	5	10
β-strand	381-385	5	10
β-strand	393-395	3	10
β-strand	413-421	9	10
β-strand	423-424	2	6
β-strand	433-435	3	6
α-helix	436-439	4
β-strand	443-457	15	10
β-strand	465-470	6	10
α-helix	476-480	5
β-strand	486-491	6	2
β-strand	495-499	5	1

Chains B, D and F: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-542	6
α-helix	574-594	21
β-strand	603-609	7	1
α-helix	619-621	3
α-helix	628-635	8
α-helix	636-638	3
α-helix	640-661	22

Chain C: 9 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	12
β-strand	45-47	3	13
β-strand	53-56	4	14
β-strand	67	1	15
β-strand	75-76	2	14
α-helix	77-78	2
β-strand	83-86	4	13
β-strand	91-94	4	16
α-helix	95-97	3
α-helix	99-115	17
β-strand	121	1	17
β-strand	129-133	5	18
β-strand	138	1	19
β-strand	154-162	9	18
β-strand	169-177	9	18
β-strand	181-183	3	18
β-strand	190-193	4	18
β-strand	201-203	3	17
α-helix	204-205	2
β-strand	209	1	15
β-strand	215	1	20
β-strand	216-218	3	14
β-strand	223-228	6	13
β-strand	236-239	4	16
β-strand	242-245	4	13
β-strand	247	1	14
β-strand	251	1	20
β-strand	259-261	3	21
β-strand	271-273	3	21
α-helix	283	1
β-strand	284-298	15	21
β-strand	304-312	7	22
β-strand	315-320	6	22
β-strand	326	1	19
β-strand	329-334	6	21
α-helix	335-353	19
β-strand	358-361	4	21
α-helix	369-372	4
β-strand	374-378	5	21
β-strand	381-385	5	21
β-strand	393-395	3	21
β-strand	413-421	9	21
β-strand	423-424	2	17
β-strand	433-435	3	17
α-helix	436-439	4
β-strand	443-457	15	21
β-strand	465-470	6	21
α-helix	476-480	5
β-strand	486-491	6	13
β-strand	494-499	6	12

Chain E: 8 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	23
β-strand	45-47	3	24
β-strand	53-56	4	25
β-strand	67	1	26
β-strand	75-76	2	25
α-helix	77-78	2
β-strand	83-86	4	24
β-strand	91-94	4	27
α-helix	99-115	17
β-strand	121	1	28
β-strand	129-133	5	29
β-strand	138	1	30
β-strand	154-162	9	29
β-strand	169-177	9	29
β-strand	181-183	3	29
β-strand	190-193	4	29
β-strand	201-203	3	28
α-helix	204-205	2
β-strand	209	1	26
β-strand	215	1	31
β-strand	216-218	3	25
β-strand	223-228	6	24
β-strand	236-239	4	27
β-strand	242-245	4	24
β-strand	247	1	25
β-strand	251	1	31
β-strand	259-261	3	32
β-strand	271-273	3	32
α-helix	283	1
β-strand	284-298	15	32
β-strand	304-312	7	33
β-strand	315-320	6	33
β-strand	326	1	30
β-strand	329-334	6	32
α-helix	335-353	19
β-strand	358-361	4	32
α-helix	369-372	4
β-strand	374-378	5	32
β-strand	381-385	5	32
β-strand	393-395	3	32
β-strand	413-421	9	32
β-strand	423-424	2	28
β-strand	433-435	3	28
α-helix	436-439	4
β-strand	443-457	15	32
β-strand	465-470	6	32
α-helix	476-480	5
β-strand	486-491	6	24
β-strand	494-499	6	23

Chains G, I and K: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	34
β-strand	10-12	3	35
β-strand	17-25	9	34
α-helix	29-31	3
β-strand	34-39	6	35
β-strand	45-51	7	35
β-strand	57-59	3	35
α-helix	61-63	3
β-strand	67-72	6	34
β-strand	77-82A	7	34
α-helix	84-86	3
β-strand	88-95	8	35
β-strand	100E-103	4	35
β-strand	104	1	34
β-strand	107-111	5	35

Chains H, J and L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	36
β-strand	10-13	4	37
β-strand	19-29	11	36
β-strand	33-38	6	37
β-strand	45-49	5	37
β-strand	53-54	2	37
α-helix	55	1
β-strand	62-65	4	36
β-strand	68-75	8	36
β-strand	85-90	6	37
α-helix	96	1
β-strand	97-98	2	37
β-strand	102-106	5	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp120	A, C, E	protein	481	Human immunodeficiency virus 1	Q2N0S6
Envelope glycoprotein gp41	B, D, F	protein	153	Human immunodeficiency virus 1	Q2N0S6
VRC34.01-COMBO1 FAB variable heavy chain	G, I, K	protein	223	Homo sapiens
VRC34.01-COMBO1 FAB variable light chain	H, J, L	protein	212	Homo sapiens

Sequence of entity 1 (A, C, E), FASTA

>8EUV_1 Envelope glycoprotein gp120 (chains A, C, E)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 2 (B, D, F), FASTA

>8EUV_2 Envelope glycoprotein gp41 (chains B, D, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (G, I, K), FASTA

>8EUV_3 VRC34.01-COMBO1 FAB variable heavy chain (chains G, I, K)
QKVLVQSGAEVKKPGASVKVSCRAFGYTFTGNALHWVRQAPGQGLEWLGWINPHSGDTFT
SQKFQGRVYMTRDKSINTAFLDVTRLTSDDTGIYYCARDKYYGNEAVGMDVWGQGTSVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 4 (H, J, L), FASTA

>8EUV_4 VRC34.01-COMBO1 FAB variable light chain (chains H, J, L)
DIQLTQSPSFLSASVGDKVTITCRASQGVRNELAWYQQKPGKAPNLLIYYASTLQSGVPS
RFSATGSGTHFTLTVSSLQPEDFATYFCQHMSSYPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15

Primary citation

Antibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site. Banach, B.B., Pletnev, S., Olia, A.S. et al. Nat Commun (2023) 14:7593-7593. DOI 10.1038/s41467-023-42098-5 · PubMed

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

8TOX 2.3 Å, Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
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…
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

Browse structure collections

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