8G4T: Vaccine-elicited human antibody 2C09

Vaccine-elicited human antibody 2C09 in complex with HIV-1 envelope trimer BG505 DS-SOSIP. Determined by electron microscopy at 2.81 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 2.81 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,739
Mol. weight: 380.89 kDa
Ligands: NAG
Released: 12 Jul 2023

Explore 8G4T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G4T contains 70 α-helices and 194 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	530-533	4
α-helix	537-541	5
α-helix	570-573	4
α-helix	576-596	21
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	620-623	4
α-helix	628-634	7
α-helix	639-663	25

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-541	5
α-helix	570-596	27
β-strand	603-609	7	2
α-helix	610-611	2
α-helix	620-623	4
α-helix	628-634	7
α-helix	639-663	25

Chain C: 11 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	3
β-strand	53-56	4	4
α-helix	58-61	4
β-strand	67	1	5
β-strand	75-76	2	4
α-helix	77-78	2
β-strand	83-86	4	3
β-strand	91-94	4	6
α-helix	99-114	16
β-strand	121	1	7
α-helix	123-125	3
β-strand	129-133	5	8
β-strand	138	1	9
β-strand	154-162	9	8
β-strand	169-177	9	8
α-helix	178-180	3
β-strand	181-183	3	8
β-strand	190-193	4	8
β-strand	202-203	2	7
α-helix	204-205	2
β-strand	209	1	5
β-strand	215	1	10
β-strand	216-218	3	4
β-strand	223-228	6	3
β-strand	236-239	4	6
β-strand	242-245	4	3
β-strand	247	1	4
α-helix	248-250	3
β-strand	251	1	10
β-strand	259-261	3	11
β-strand	271-273	3	11
β-strand	284-302	19	11
β-strand	304-312	7	12
β-strand	315-320	6	12
β-strand	326	1	9
β-strand	329-334	6	11
α-helix	335-349	15
α-helix	350-352	3
β-strand	358-361	4	11
β-strand	374-378	5	11
β-strand	381-385	5	11
β-strand	393-395	3	11
β-strand	413-421	9	11
β-strand	423-424	2	7
β-strand	434-435	2	7
α-helix	436-438	3
β-strand	441-456	16	11
β-strand	465-470	6	11
α-helix	476-480	5
β-strand	486-491	6	3
β-strand	494-499	6	1

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	38
β-strand	11-12	2	39
β-strand	17-25	9	38
α-helix	29-31	3
β-strand	34-39	6	40
β-strand	45-51	7	40
β-strand	57-59	3	40
β-strand	67-72	6	38
β-strand	77-82A	7	38
β-strand	88-95	8	40
β-strand	100C-102	3	40
β-strand	107-109	3	40
β-strand	110-111	2	39

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	41
β-strand	10-13	4	42
β-strand	20-25	6	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	62-67	6	41
β-strand	70-75	6	41
β-strand	85-90	6	42
α-helix	96	1
β-strand	97-98	2	42
β-strand	102-106	5	42

Chain F: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-541	5
α-helix	576-596	21
β-strand	603-609	7	13
α-helix	610-611	2
α-helix	620-623	4
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	2
β-strand	45-47	3	14
β-strand	53-56	4	15
α-helix	58-61	4
β-strand	67	1	16
α-helix	71-73	3
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	99-114	16
β-strand	121	1	18
α-helix	123-125	3
β-strand	129-133	5	19
β-strand	138	1	20
β-strand	154-162	9	19
β-strand	169-177	9	19
β-strand	181-183	3	19
β-strand	190-193	4	19
β-strand	202-203	2	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
α-helix	248-250	3
β-strand	251	1	21
β-strand	259-261	3	22
β-strand	271-274	4	22
β-strand	284-298	15	22
β-strand	304-312	7	23
β-strand	315-320	6	23
β-strand	326	1	20
β-strand	329-334	6	22
α-helix	335-349	15
α-helix	350-352	3
β-strand	358-361	4	22
β-strand	374-378	5	22
β-strand	381-385	5	22
β-strand	393-395	3	22
β-strand	413-421	9	22
β-strand	423-424	2	18
α-helix	426-428	3
β-strand	434-435	2	18
α-helix	436-438	3
β-strand	443-456	14	22
β-strand	465-470	6	22
α-helix	476-480	5
β-strand	486-491	6	14
β-strand	494-499	6	2

Chain H: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	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
β-strand	67-72	6	34
β-strand	77-82A	7	34
β-strand	88-95	8	35
β-strand	100C-102	3	35
β-strand	107-111	5	35

4 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 BG505 DS-SOSIP gp41	A, B, F	protein	153	Human immunodeficiency virus 1	Q2N0S7
Envelope glycoprotein BG505 DS-SOSIP gp120	C, G, I	protein	473	Human immunodeficiency virus 1	Q2N0S6
Fab 2C09 heavy chain	D, H, J	protein	232	Homo sapiens
Fab 2C09 light chain	E, K, L	protein	214	Homo sapiens

Sequence of entity 1 (A, B, F), FASTA

>8G4T_1 Envelope glycoprotein BG505 DS-SOSIP gp41 (chains A, B, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (C, G, I), FASTA

>8G4T_2 Envelope glycoprotein BG505 DS-SOSIP gp120 (chains C, G, I)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

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

>8G4T_3 Fab 2C09 heavy chain (chains D, H, J)
EVQLVESGEGLVQPGGSLRLSCAASGFTFSSHAMHWVRQAPGKGLEYVSAISSEGGSTYY
ADSVRGRFIISRDNSKNTLYLQMGSLRAEDMAVYYCARVTGDYNWYFDLWGRGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

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

>8G4T_4 Fab 2C09 light chain (chains E, K, L)
EIVMTQSPATLSVSPGERATLSCRASQGVSSNLAWYQQKPGQAPRLLIHGASTRATGSPA
RFSGSGSGTEFTLTISSLQSEDFAVYSCQQYHNWPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

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 Q2N0S7), best resolution first:

5I8C 1.54 Å, Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex…
6WX2 2.39 Å, Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with F60P mutation on…
8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
8G4M 2.95 Å, Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6MPG 3.2 Å, Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody,…
6UM7 3.5 Å, Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex…
9PNN 3.5 Å, Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
6CM3 3.54 Å, BG505 SOSIP in complex with sCD4, 17b, 8ANC195
6CDI 3.6 Å, Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex…
8DOW 3.69 Å, Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
7LL1 3.73 Å, Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly…

Browse structure collections

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