6V8X: Envelope glycoprotein gp120

VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure. Determined by electron microscopy at 3.0 Å resolution. Released 5 Feb 2020.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 24,825
Mol. weight: 371.13 kDa
Ligands: NAG
Released: 5 Feb 2020

Explore 6V8X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V8X contains 83 α-helices and 300 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, E and I: 9 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	55-56	2	3
β-strand	67	1	4
β-strand	75-76	2	3
α-helix	77-78	2
β-strand	84-86	3	2
β-strand	91-92	2	5
α-helix	100-114	15
α-helix	123-125	3
β-strand	130-133	4	6
β-strand	149	1	7
β-strand	154-158	5	6
β-strand	159-162	4	8
β-strand	169-172	4	8
β-strand	175-177	3	6
α-helix	178-180	3
β-strand	181-183	3	9
β-strand	189-190	2	6
β-strand	191-193	3	9
β-strand	200-203	4	10
α-helix	204-205	2
β-strand	209	1	4
β-strand	215	1	11
β-strand	216	1	3
β-strand	218	1	12
β-strand	223-228	6	2
β-strand	238-239	2	5
β-strand	242-245	4	2
β-strand	247	1	12
β-strand	251	1	11
β-strand	259-261	3	13
β-strand	271-273	3	13
β-strand	284-297	14	13
β-strand	302	1	14
β-strand	304-308	5	15
β-strand	316-320	5	15
β-strand	326	1	7
β-strand	330-334	5	13
α-helix	342-353	12
β-strand	358-361	4	13
α-helix	369-372	4
β-strand	374	1	16
β-strand	383-385	3	16
β-strand	393-395	3	13
β-strand	413-415	3	13
β-strand	418-420	3	16
β-strand	423-424	2	10
β-strand	432-435	4	10
α-helix	436-438	3
β-strand	441	1	14
β-strand	444-456	13	13
β-strand	465-470	6	13
α-helix	475-477	3
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains B, F and J: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	537-541	5
α-helix	567-595	29
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	612-614	3
α-helix	620-623	4
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-645	7
α-helix	647-663	17

Chain C: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	17
β-strand	5	1	18
β-strand	11-12	2	19
β-strand	19-23	5	18
β-strand	34-39	6	20
β-strand	46-51	6	20
β-strand	57-59	3	20
α-helix	61-63	3
β-strand	67-72	6	18
β-strand	77-82	6	18
α-helix	84-86	3
β-strand	89-91	3	20
β-strand	94	1	20
β-strand	102	1	20
β-strand	104	1	17
β-strand	110-111	2	19
β-strand	121-123	3	21
β-strand	124	1	22
β-strand	136-137	2	23
β-strand	140-142	3	21
β-strand	145	1	24
β-strand	153-154	2	25
β-strand	163-164	2	26
α-helix	166-168	3
β-strand	169-170	2	24
β-strand	176-177	2	24
β-strand	181-182	2	26
β-strand	183-184	2	23
β-strand	195-200	6	25
α-helix	201-203	3
β-strand	205-210	6	25

Chains D, H and L: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	27
β-strand	10-13	4	28
β-strand	19-24	6	27
β-strand	34-38	5	28
β-strand	45-49	5	28
β-strand	53-54	2	28
α-helix	55	1
β-strand	62-65	4	27
β-strand	70-75	6	27
α-helix	80-82	3
β-strand	85-89	5	28
β-strand	90	1	29
β-strand	97	1	29
β-strand	102-106	5	28
β-strand	117-118	2	30
α-helix	121	1
β-strand	122	1	22
α-helix	123	1
β-strand	131	1	31
β-strand	137-141	5	30
β-strand	150-152	3	32
β-strand	156	1	32
β-strand	169	1	33
β-strand	174	1	33
β-strand	175-177	3	30
β-strand	184	1	31
α-helix	188-191	4
β-strand	194-196	3	32
β-strand	198	1	34
β-strand	207	1	34

Chains G and K: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	51
β-strand	5	1	52
β-strand	11-12	2	53
β-strand	19-23	5	52
α-helix	29-31	3
β-strand	34-39	6	54
β-strand	46-51	6	54
β-strand	57-59	3	54
α-helix	61-63	3
β-strand	67-72	6	52
β-strand	77-82	6	52
α-helix	84-86	3
β-strand	89-91	3	54
β-strand	94	1	54
β-strand	102	1	54
β-strand	104	1	51
β-strand	110-111	2	53
β-strand	121-123	3	55
β-strand	124	1	56
β-strand	136-137	2	57
β-strand	140-142	3	55
β-strand	145	1	58
β-strand	153-154	2	59
β-strand	163-164	2	60
α-helix	166-168	3
β-strand	169-170	2	58
β-strand	176-177	2	58
β-strand	181-182	2	60
β-strand	183-184	2	57
β-strand	195-200	6	59
α-helix	201-203	3
β-strand	205-210	6	59

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp120	A, E, I	protein	471	Human immunodeficiency virus 1	Q2N0S6
Envelope glycoprotein gp41	B, F, J	protein	145	Human immunodeficiency virus 1	Q2N0S9
VRC01 Fab Heavy Chain	C, G, K	protein	224	Homo sapiens	Q6N095 (AlphaFold model)
VRC01 Fab Light Chain	D, H, L	protein	208	Homo sapiens	Q6PIL8 (AlphaFold model)

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

>6V8X_1 Envelope glycoprotein gp120 (chains A, E, I)
NLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNIWATHACVPTDPNPQEIHLENVTEE
FNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCSFN
MTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQVCPKLSFEP
IPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVLSTQLLLNGSLAEEEVMI
RSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNV
SKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNS
TWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLIL
TRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

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

>6V8X_2 Envelope glycoprotein gp41 (chains B, F, J)
LGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVWGIKQLQAR
VLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYT
QIIYGLLEESQNQQEKNEQDLLALD

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

>6V8X_3 VRC01 Fab Heavy Chain (chains C, G, K)
QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNY
ARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVS
SPSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC

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

>6V8X_4 VRC01 Fab Light Chain (chains D, H, L)
VLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSG
SRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLK
SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY
EKHKVYACEVTHQGLRSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements. Henderson, R., Lu, M., Zhou, Y. et al. Nat Commun (2020) 11:520-520. DOI 10.1038/s41467-019-14196-w · 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
8EUU 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB

Browse structure collections

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