9PNN: J601-A6 Fab

Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer. Determined by electron microscopy at 3.5 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Human immunodeficiency virus 1, Macaca mulatta
Chains: 12
Atoms: 21,225
Mol. weight: 388.17 kDa
Ligands: NAG
Released: 17 Dec 2025

Explore 9PNN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PNN contains 81 α-helices and 216 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, B and F: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	519	1	20
α-helix	523-525	3
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-543	7
α-helix	572-595	24
β-strand	603-609	7	21
α-helix	619-625	7
α-helix	628-635	8
α-helix	639-663	25

Chains C, G and I: 14 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	21
β-strand	45-47	3	22
β-strand	53-56	4	23
α-helix	58-61	4
β-strand	67	1	24
β-strand	75-76	2	23
α-helix	77-78	2
β-strand	83-86	4	22
β-strand	91-94	4	25
α-helix	99-116	18
α-helix	120	1
β-strand	121	1	26
β-strand	129-133	5	27
β-strand	138	1	28
α-helix	140-150	3
β-strand	154-162	9	27
β-strand	169-177	9	27
α-helix	178-180	3
β-strand	181-184	4	27
β-strand	190-193	4	27
β-strand	202	1	26
α-helix	203-205	3
β-strand	209	1	24
β-strand	215	1	29
β-strand	216-218	3	23
β-strand	223-228	6	22
β-strand	236-239	4	25
β-strand	242-245	4	22
β-strand	247	1	23
α-helix	248-250	3
β-strand	251	1	29
β-strand	256	1	30
β-strand	260-261	2	31
β-strand	271-274	4	31
β-strand	284-300	17	31
β-strand	301	1	32
β-strand	302	1	31
β-strand	304-312	7	27
β-strand	315-320	6	27
α-helix	321A-322	2
β-strand	323	1	32
β-strand	326	1	28
β-strand	330-334	5	31
α-helix	335-353	19
β-strand	358-361	4	31
α-helix	369-372	4
β-strand	374-378	5	30
β-strand	381-385	5	30
α-helix	387-389	3
β-strand	393-395	3	31
β-strand	413-417	5	31
β-strand	418-420	3	30
β-strand	423-424	2	33
β-strand	434-435	2	33
α-helix	436-438	3
β-strand	441-456	16	31
β-strand	465-470	6	31
α-helix	475-480	6
β-strand	486-491	6	22
β-strand	495-499	5	21

Chains D, H and J: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	34
β-strand	11-12	2	35
β-strand	18-23	6	34
β-strand	31	1	20
β-strand	35-39	7	36
β-strand	46-52	7	36
β-strand	57-59	3	36
α-helix	61-63	3
β-strand	67-72	6	34
β-strand	77-82	6	34
α-helix	84-86	3
β-strand	88-95	8	36
β-strand	102	1	36
β-strand	107-109	3	36
β-strand	110-111	2	35

Chains E, K and L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	37
β-strand	10-13	4	38
β-strand	19-25	7	37
β-strand	33-38	6	38
β-strand	45-49	5	38
β-strand	53-54	2	38
α-helix	55	1
β-strand	62-67	6	37
β-strand	70-75	6	37
α-helix	80-82	3
β-strand	85-90	6	38
α-helix	96	1
β-strand	98	1	38
β-strand	102-106	5	38

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
antibody J601-A6 heavy chain	D, H, J	protein	234	Macaca mulatta
antibody J601-A6 light chain	E, K, L	protein	215	Macaca mulatta

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

>9PNN_1 Envelope glycoprotein BG505 DS-SOSIP gp41 (chains A, B, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>9PNN_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

>9PNN_3 antibody J601-A6 heavy chain (chains D, H, J)
QVQLEESGPGIVKPSETLSLTCAASRGPFSGGHFYWNWFRQPPGKGLEWIGGIYSDGDAA
DYNPSLESRVAISRDRSANRFSLKLISVTATDTAVYYCSSTYSWNNVWFDQWGQGVLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

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

>9PNN_4 antibody J601-A6 light chain (chains E, K, L)
EDIQLTQSPSSLSASVGDRVTITCRASQDINTDLSWYYQKSGEAPKLLIYRASNLQSGAP
SRFSGTGSGTEFTLTISSLQPEDFITYYCQQRYSFPITFGAGTKVDIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Vaccine elicitation of HIV-1 neutralizing antibodies against both V2 apex and fusion peptide in rhesus macaques. Duan, H., Nkolola, J.P., Wang, S. et al. Cell Rep (2026) 45:116905-116905. DOI 10.1016/j.celrep.2025.116905 · 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
8G4T 2.81 Å, Vaccine-elicited human antibody 2C09 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…
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…

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