6V8Z: Envelope glycoprotein gp120

VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure. Determined by electron microscopy at 2.9 Å resolution. Released 5 Feb 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 18
Atoms: 35,877
Mol. weight: 522.12 kDa
Ligands: NAG
Released: 5 Feb 2020

Explore 6V8Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V8Z contains 114 α-helices and 414 β-strands across 18 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, G and M: 11 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53	1	3
β-strand	56	1	4
α-helix	65-66	2
α-helix	76-78	3
β-strand	84-85	2	2
α-helix	86	1
β-strand	91-94	4	5
α-helix	100-115	16
α-helix	120	1
β-strand	121	1	6
β-strand	129-130	2	7
β-strand	132-133	2	8
β-strand	154-162	9	8
β-strand	169-177	9	8
α-helix	178-180	3
β-strand	181-183	3	7
β-strand	188-193	4	7
β-strand	200-201	2	9
β-strand	202	1	6
α-helix	203-205	3
β-strand	215	1	4
β-strand	218	1	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	4
β-strand	259-261	3	10
β-strand	271-273	3	10
β-strand	284-287	4	10
β-strand	292-298	7	10
β-strand	302-304	3	11
β-strand	307-312	4	12
β-strand	315-317	3	12
β-strand	320-323	4	11
β-strand	330-334	5	10
α-helix	335-353	19
β-strand	358-361	4	10
α-helix	369-372	4
β-strand	374-375	2	13
β-strand	378	1	14
β-strand	381	1	14
β-strand	383-385	3	13
β-strand	393-395	3	10
β-strand	413-417	5	10
β-strand	418-420	3	13
β-strand	432-433	2	9
α-helix	436-439	4
β-strand	443-456	14	10
β-strand	465-470	6	10
α-helix	476-479	4
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains B, H and N: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	524-526	3
α-helix	539-545	7
α-helix	548-550	3
α-helix	552-554	3
α-helix	567-584	18
α-helix	587-595	9
β-strand	603-609	7	1
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-646	8
α-helix	651	1
α-helix	652-657	6
α-helix	658-663	6

Chains C, I and O: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	10-12	3	30
β-strand	17-25	9	29
β-strand	34-40	7	30
β-strand	44-52	9	30
β-strand	56-59	4	30
β-strand	67-68	2	29
β-strand	71-73	3	29
β-strand	76F-82A	9	29
α-helix	84-86	3
β-strand	88-95	8	30
β-strand	100F-102	3	30
β-strand	107-111	5	30
α-helix	114-116	3
β-strand	117	1	31
β-strand	122-124	3	32
β-strand	131-141	11	32
β-strand	142	1	31
β-strand	146	1	33
β-strand	149-150	2	33
β-strand	159-161	3	32
α-helix	163-164	2
β-strand	165-168	4	32
β-strand	171-181	11	32
α-helix	184-186	3
β-strand	190-196	7	33
α-helix	197-199	3
β-strand	201-207	7	33

Chains D, J and P: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	15
β-strand	11-12	2	16
β-strand	20-24	5	15
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	46-51	6	17
β-strand	58-59	2	17
β-strand	67-71	5	15
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-99	12	17
β-strand	100L-103	8	17
β-strand	107-109	3	17
β-strand	110-111	2	16
β-strand	117	1	18
β-strand	120-124	5	19
α-helix	125-126	2
β-strand	131-133	3	20
β-strand	134-140	7	19
β-strand	141	1	18
β-strand	146-149	4	21
β-strand	154	1	21
β-strand	158-160	3	20
α-helix	161-163	3
β-strand	164-165	2	19
α-helix	166	1
β-strand	171-174	4	19
β-strand	175-179	5	20
α-helix	181-184	4
β-strand	190-195	6	21
β-strand	200-205	6	21

Chains E, K and Q: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	6	22
β-strand	19-22	4	23
β-strand	32-38	7	22
β-strand	40	1	24
β-strand	42	1	24
β-strand	44-48	5	22
β-strand	49	1	25
β-strand	53	1	25
β-strand	62-63	2	23
β-strand	72-75	4	23
α-helix	80-82	3
β-strand	85-86	2	22
β-strand	88-91	4	22
β-strand	102-106A	6	22
β-strand	115-119	5	26
β-strand	134-138	5	26
β-strand	146-150	5	27
β-strand	155	1	27
β-strand	160-162	3	28
β-strand	166-167	2	26
β-strand	173-176	4	26
β-strand	177-179	3	28
α-helix	183-186	4
β-strand	192-198	7	27
β-strand	201-207	7	27

Chains F, L and R: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	34
β-strand	10-13	4	35
β-strand	19-24	6	34
β-strand	34-38	5	35
β-strand	45-49	5	35
β-strand	53-54	2	35
β-strand	62-67	6	34
β-strand	70-75	6	34
β-strand	85-90	6	35
β-strand	97-98	2	35
β-strand	102-106	5	35
β-strand	116-118	3	36
α-helix	122-125	4
β-strand	129-130	2	37
β-strand	133-139	7	36
β-strand	147-150	4	38
β-strand	162-163	2	36
β-strand	173-177	5	36
β-strand	181-182	2	37
α-helix	183-186	4
β-strand	192-195	4	38
β-strand	196	1	39
β-strand	205	1	39
β-strand	208	1	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp120	A, G, M	protein	472	Human immunodeficiency virus 1	Q2N0S6
envelope glycoprotein gp41	B, H, N	protein	147	Human immunodeficiency virus 1	Q2N0S7
10-1074 Fab Heavy Chain	D, J, P	protein	235	Homo sapiens	Q6N089 (AlphaFold model)
10-1074 Fab Light Chain	E, K, Q	protein	211	Homo sapiens	Q8N5F4 (AlphaFold model)
VRC03 Fab Heavy Chain	C, I, O	protein	231	Homo sapiens	P0DOX5
VRC03 Fab Light Chain	F, L, R	protein	208	Homo sapiens	Q6P5S8

Sequence of entity 1 (A, G, M), FASTA

>6V8Z_1 Envelope glycoprotein gp120 (chains A, G, M)
ENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNIWATHACVPTDPNPQEIHLENVTE
EFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCSF
NMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITMVCPKLSFE
PIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVLSTQLLLNGSLAEEEVM
IRSENITNNAKNILVQFNTPVQINCTRPLNLTRKSIRIGPGQAFYAMGDIIGDIRQAHCN
VSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFN
STWISNTSVQGSNSTGSNDSITLPCRIKMIINMWQRIGQAMYAPPIQGVIRCVSNITGLI
LTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

Sequence of entity 2 (B, H, N), FASTA

>6V8Z_2 envelope glycoprotein gp41 (chains B, H, N)
VFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQ
ARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISN
YTQIIYGLLEESQNQQEKNEQDLLALD

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

>6V8Z_3 10-1074 Fab Heavy Chain (chains D, J, P)
QVQLQESGPGLVKPSETLSVTCSVSGDSMNNYYWTWIRQSPGKGLEWIGYISDRESATYN
PSLNSRVVISRDTSKNQLSLKLNSVTPADTAVYYCATARRGQRIYGVVSFGEFFYYYSMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

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

>6V8Z_4 10-1074 Fab Light Chain (chains E, K, Q)
VRPLSVALGETARISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERFSGTPD
INFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSVTLFPP
SSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSL
TPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Sequence of entity 5 (C, I, O), FASTA

>6V8Z_5 VRC03 Fab Heavy Chain (chains C, I, O)
QVQLVQSGAVIKTPGSSVKISCRASGYNFRDYSIHWVRLIPDKGFEWIGWIKPLWGAVSY
ARQLQGRVSMTRQLSQDPDDPDWGVAYMEFSGLTPADTAEYFCVRRGSCDYCGDFPWQYW
CQGTVVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 6 (F, L, R), FASTA

>6V8Z_6 VRC03 Fab Light Chain (chains F, L, R)
EIVLTQSPGILSLSPGETATLFCKASQGGNAMTWYQKRRGQVPRLLIYDTSRRASGVPDR
FVGSGSGTDFFLTINKLDREDFAVYYCQQFEFFGLGSELEVHRTVAAPSVFIFPPSDEQL
KSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKAD
YEKHKVYACEVTHQGLSSPVTKSFNRGE

Ligands and cofactors

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

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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