8G4M: Vaccine-elicited human antibody 2C06

Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP. Determined by electron microscopy at 2.95 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 2.95 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,584
Mol. weight: 380.5 kDa
Ligands: NAG
Released: 12 Jul 2023

Explore 8G4M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G4M contains 81 α-helices and 198 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	524-526	3
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-541	5
α-helix	570-595	26
β-strand	603-609	7	1
α-helix	619-623	5
α-helix	628-634	7
α-helix	639-662	24

Chain B: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-541	5
α-helix	570-595	26
β-strand	603-609	7	12
α-helix	610-611	2
α-helix	620-623	4
α-helix	628-634	7
α-helix	639-663	25

Chain C: 16 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
α-helix	52	1
β-strand	53-56	4	3
β-strand	67	1	4
α-helix	71-73	3
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	99-116	18
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
α-helix	194-197	4
β-strand	202-203	2	6
α-helix	204-205	2
β-strand	209	1	4
β-strand	215	1	9
β-strand	216-218	3	3
α-helix	219-220	2
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	256	1	10
β-strand	259-261	3	10
α-helix	264-266	3
β-strand	271-274	4	10
β-strand	284-302	19	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	335-349	15
α-helix	350-352	3
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
α-helix	426-428	3
β-strand	434-435	2	6
α-helix	436-438	3
β-strand	441-456	16	10
β-strand	465-470	6	10
α-helix	476-480	5
α-helix	483-485	3
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains D and J: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	35
β-strand	11-12	2	36
β-strand	17-25	9	35
α-helix	29-31	3
β-strand	34-39	6	37
β-strand	45-51	7	37
β-strand	57-59	3	37
β-strand	67-72	6	35
β-strand	77-82A	7	35
α-helix	84-86	3
β-strand	88-95	8	37
β-strand	100G-103	4	37
β-strand	107-109	3	37
β-strand	110-111	2	36

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	38
β-strand	10-13	4	39
β-strand	19-25	7	38
β-strand	33-38	6	39
β-strand	45-49	5	39
β-strand	53-54	2	39
α-helix	55	1
β-strand	62-67	6	38
β-strand	70-75	6	38
β-strand	85-90	6	39
α-helix	96	1
β-strand	97-98	2	39
β-strand	102-106	5	39

Chain F: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	524-527	4
β-strand	529	1	34
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-541	5
α-helix	570-595	26
β-strand	603-609	7	23
α-helix	610-611	2
α-helix	619-623	5
β-strand	627	1	34
α-helix	628-634	7
α-helix	639-663	25

Chain G: 13 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	99-116	18
α-helix	120	1
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
α-helix	178-180	3
β-strand	181-183	3	18
β-strand	189-193	5	18
α-helix	194-197	4
β-strand	202-203	2	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
α-helix	264-266	3
β-strand	271-274	4	21
β-strand	284-302	19	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	335-349	15
α-helix	357	1
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
α-helix	426-428	3
β-strand	434-435	2	17
α-helix	436-438	3
β-strand	441-456	16	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 H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	40
β-strand	11-12	2	41
β-strand	18-25	8	40
α-helix	29-31	3
β-strand	34-39	6	42
β-strand	45-51	7	42
β-strand	57-59	3	42
β-strand	67-72	6	40
β-strand	77-82	6	40
α-helix	84-86	3
β-strand	88-95	8	42
β-strand	100G-103	4	42
β-strand	107-109	3	42
β-strand	110-111	2	41

3 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	C, G, I	protein	473	Human immunodeficiency virus 1	Q2N0S6
Envelope glycoprotein gp41	A, B, F	protein	153	Human immunodeficiency virus 1	Q2N0S7
antibody heavy chain	D, H, J	protein	236	Homo sapiens
antibody light chain	E, K, L	protein	214	Homo sapiens

Sequence of entity 1 (C, G, I), FASTA

>8G4M_1 Envelope glycoprotein gp120 (chains C, G, I)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

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

>8G4M_2 Envelope glycoprotein gp41 (chains A, B, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>8G4M_3 antibody heavy chain (chains D, H, J)
EVQLVESGGGLVQPGGSLRLSCSASGFTFSSYAMHWVRQAPGKGLEYVSAISGNGDSTYY
ADSVRGRFTISRDNSKNTLYLQMSSLRAEDTAVYYCVKQAAYCTRTSCYYFDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

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

>8G4M_4 antibody light chain (chains E, K, L)
EIVMTQSPATLSVSPGERATLSCRASQGVSSKLAWYQQKPGQAPRLLIYGASTRATGIPA
RFSGSGSGTEFTLTISSLQSEDFAVYYCQQYHNWPYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

HIV-1 neutralizing antibodies elicited in humans by a prefusion-stabilized envelope trimer form a reproducible class targeting fusion peptide. Wang, S., Matassoli, F., Zhang, B. et al. Cell Rep (2023) 42:112755-112755. DOI 10.1016/j.celrep.2023.112755 · 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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