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

Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB. Determined by electron microscopy at 2.7 Å resolution. Released 27 Sept 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 19,926
Mol. weight: 372.5 kDa
Ligands: NAG
Released: 27 Sept 2023

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

Secondary structure: helices and β-sheets

8EUU contains 79 α-helices and 202 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: 10 helices, 42 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	95-97	3
α-helix	99-114	16
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
α-helix	178-180	3
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
α-helix	248-250	3
β-strand	251	1	9
β-strand	260-261	2	10
β-strand	271-273	3	10
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	330-334	5	10
α-helix	335-353	19
β-strand	358-361	4	10
α-helix	369-372	4
β-strand	374-378	5	12
β-strand	381-385	5	12
β-strand	393-395	3	10
β-strand	413-417	5	10
β-strand	418-421	4	12
β-strand	423-424	2	6
β-strand	433-435	3	6
α-helix	436-439	4
β-strand	443-456	14	10
β-strand	465-470	6	10
α-helix	475-483	9
β-strand	486-491	6	2
β-strand	495-499	5	1

Chains B and D: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	524-526	3
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-542	6
α-helix	571-595	25
β-strand	603-609	7	1
α-helix	619-621	3
α-helix	628-635	8
α-helix	636-638	3
α-helix	640-662	23

Chain C: 11 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	13
β-strand	45-47	3	14
β-strand	53-56	4	15
β-strand	67	1	16
β-strand	75-76	2	15
α-helix	77-78	2
β-strand	83-86	4	14
β-strand	91-94	4	17
α-helix	95-97	3
α-helix	99-116	18
β-strand	121	1	18
β-strand	129-133	5	19
β-strand	138	1	20
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	200	1
β-strand	201-203	3	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	22
β-strand	271-273	3	22
α-helix	283	1
β-strand	284-298	15	22
β-strand	301	1	23
β-strand	304-312	7	24
β-strand	315-320	6	24
β-strand	323	1	23
β-strand	326	1	20
β-strand	330-334	5	22
α-helix	335-353	19
β-strand	358-361	4	22
α-helix	369-372	4
β-strand	374-378	5	25
β-strand	381-385	5	25
β-strand	393-395	3	22
β-strand	413-417	5	22
β-strand	418-421	4	25
β-strand	423-424	2	18
β-strand	433-435	3	18
α-helix	436-439	4
β-strand	443-457	15	22
β-strand	465-470	6	22
α-helix	475-483	9
β-strand	486-491	6	14
β-strand	495-499	5	13

Chain E: 12 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	26
β-strand	45-47	3	27
β-strand	53-56	4	28
β-strand	67	1	29
β-strand	75-76	2	28
α-helix	77-78	2
β-strand	83-86	4	27
β-strand	91-94	4	30
α-helix	95-97	3
α-helix	99-116	18
β-strand	121	1	31
β-strand	129-133	5	32
β-strand	138	1	33
β-strand	154-162	9	32
β-strand	169-177	9	32
α-helix	178-180	3
β-strand	181-183	3	32
β-strand	190-193	4	32
α-helix	194-197	4
α-helix	200	1
β-strand	201-203	3	31
α-helix	204-205	2
β-strand	209	1	29
β-strand	215	1	34
β-strand	216-218	3	28
β-strand	223-228	6	27
β-strand	236-239	4	30
β-strand	242-245	4	27
β-strand	247	1	28
α-helix	248-250	3
β-strand	251	1	34
β-strand	256	1	35
β-strand	260-261	2	36
β-strand	271-274	4	36
β-strand	284-298	15	36
β-strand	301	1	37
β-strand	304-312	7	38
β-strand	315-320	6	38
β-strand	323	1	37
β-strand	326	1	33
β-strand	330-334	5	36
α-helix	335-353	19
β-strand	358-361	4	36
α-helix	369-372	4
β-strand	374-378	5	35
β-strand	381-385	5	35
β-strand	393-395	3	36
β-strand	413-417	5	36
β-strand	418-421	4	35
β-strand	423-424	2	31
β-strand	433-435	3	31
α-helix	436-439	4
β-strand	443-456	14	36
β-strand	465-470	6	36
α-helix	476-483	8
β-strand	486-491	6	27
β-strand	495-499	5	26

Chain F: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-542	6
α-helix	571-595	25
β-strand	603-609	7	26
α-helix	619-621	3
α-helix	628-635	8
α-helix	636-638	3
α-helix	640-662	23

Chain G: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	39
α-helix	7-9	3
β-strand	10-12	3	40
β-strand	17-25	9	39
α-helix	29-31	3
β-strand	34-39	6	40
β-strand	45-51	7	40
β-strand	57-59	3	40
α-helix	61-63	3
β-strand	67-72	6	39
β-strand	77-82A	7	39
β-strand	88-95	8	40
α-helix	98-100	3
β-strand	100E-103	4	40
β-strand	104	1	39
β-strand	107-111	5	40

Chains H, J and L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	41
β-strand	10-13	4	42
β-strand	19-29	11	41
β-strand	33-38	6	42
β-strand	45-49	5	42
β-strand	53-54	2	42
α-helix	55	1
β-strand	62-65	4	41
β-strand	68-75	8	41
α-helix	80-82	3
β-strand	85-90	6	42
α-helix	96	1
β-strand	97-98	2	42
β-strand	102-106	5	42

Chain I: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	43
β-strand	10-12	3	44
β-strand	17-25	9	43
α-helix	29-31	3
β-strand	34-39	6	44
β-strand	45-51	7	44
β-strand	57-59	3	44
α-helix	61-63	3
β-strand	67-72	6	43
β-strand	77-82A	7	43
β-strand	88-95	8	44
α-helix	98-100	3
β-strand	100E-103	4	44
β-strand	107-111	5	44

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

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 FAB variable heavy chain	G, I, K	protein	223	Homo sapiens
VRC34.01 FAB variable light chain	H, J, L	protein	212	Homo sapiens

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

>8EUU_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

>8EUU_2 Envelope glycoprotein gp41 (chains B, D, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>8EUU_3 VRC34.01 FAB variable heavy chain (chains G, I, K)
QEVLVQSGAEVKKPGASVKVSCRAFGYTFTGNALHWVRQAPGQGLEWLGWINPHSGDTTT
SQKFQGRVYMTRDKSINTAFLDVTRLTSDDTGIYYCARDKYYGNEAVGMDVWGQGTSVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

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

>8EUU_4 VRC34.01 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…
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
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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