9P6E: N49P7-FR Fab

N49P7-FR Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab. Determined by electron microscopy at 2.7 Å resolution. Released 29 Apr 2026.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Human immunodeficiency virus 1, Macaca mulatta, Homo sapiens
Chains: 18
Atoms: 24,678
Mol. weight: 380.07 kDa
Ligands: NAG
Released: 29 Apr 2026

Explore 9P6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9P6E contains 105 α-helices and 273 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, C and E: 16 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53-55	3	3
β-strand	67	1	4
β-strand	75	1	3
α-helix	76-78	3
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
α-helix	123-125	3
β-strand	129-133	5	7
β-strand	138	1	8
α-helix	140-150	3
β-strand	154-162	9	7
β-strand	169-177	9	7
α-helix	178-180	3
β-strand	181-183	3	7
β-strand	190-193	4	7
β-strand	200-203	4	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	7
β-strand	259-261	3	7
α-helix	264-266	3
β-strand	271-274	4	7
β-strand	284-312	27	7
β-strand	315-323A	10	7
β-strand	326	1	8
β-strand	329-334	6	7
α-helix	335-353	19
β-strand	358-361	4	7
α-helix	369-372	4
β-strand	374-378	5	7
β-strand	381-385	5	7
α-helix	387-389	3
β-strand	393-395	3	7
β-strand	413-421	9	7
β-strand	423-424	2	6
α-helix	426-428	3
β-strand	432-435	4	6
α-helix	436-439	4
β-strand	441-456	16	7
α-helix	457	1
β-strand	465-470	6	7
α-helix	476-483	8
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains B, D and F: 11 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	571-595	25
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	619	1
α-helix	620-624	5
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-660	22

Chains G, J and O: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-11	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	57-59	3	11
α-helix	61-63	3
β-strand	67-72	6	10
β-strand	77-82	6	10
α-helix	84-86	3
β-strand	88-95	8	11
β-strand	100H-103	4	11
β-strand	107-110	4	11

Chains H, K and P: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
β-strand	10-12	3	17
β-strand	15-25	11	16
α-helix	29-31	3
β-strand	32-39	8	17
β-strand	45-52	8	17
β-strand	56-58	3	17
α-helix	61-63	3
β-strand	64	1	16
β-strand	67-73	7	16
β-strand	76G-82C	10	16
α-helix	84-86	3
β-strand	88-99	12	17
β-strand	100K-103	4	17
β-strand	107-111	5	17

Chains I, M and Q: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
β-strand	5	1	13
β-strand	9-12	3	14
β-strand	19-24	6	13
β-strand	33-38	6	14
β-strand	45-48	4	14
β-strand	49	1	15
β-strand	53	1	15
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-91	7	14
β-strand	96-98	3	14
β-strand	99	1	12
β-strand	102-105	4	14

Chains L, N and R: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	18
β-strand	9	1	17
β-strand	18-24	7	18
β-strand	34-38	5	17
α-helix	43-44	2
β-strand	45-48	4	17
β-strand	49	1	19
β-strand	53	1	19
β-strand	62-67	6	18
β-strand	70-76	7	18
β-strand	85-90	6	17
β-strand	97-98	2	17
β-strand	102-103	2	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp120	A, C, E	protein	481	Human immunodeficiency virus 1	Q2N0S5
Envelope glycoprotein gp41	B, D, F	protein	153	Human immunodeficiency virus 1	Q2N0S6
RM20A3 heavy chain	G, J, O	protein	125	Macaca mulatta
RM20A3 light chain	I, M, Q	protein	109	Macaca mulatta
N49P7-FR heavy chain	H, K, P	protein	134	Homo sapiens
N49P7-FR light chain	L, N, R	protein	99	Homo sapiens

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

>9P6E_1 Envelope glycoprotein gp120 (chains A, C, E)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
IIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

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

>9P6E_2 Envelope glycoprotein gp41 (chains B, D, F)
AVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHW
GIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (G, J, O), FASTA

>9P6E_3 RM20A3 heavy chain (chains G, J, O)
EVQLVETGGGLVQPGGSLKLSCRASGYTFSSFAMSWVRQAPGKGLEWVSLINDRGGLTFY
VDSVKGRFTISRDNSKNTLSLQMHSLRDGDTAVYYCATGGMSSALQSSKYYFDFWGQGAL
VTVSS

Sequence of entity 4 (I, M, Q), FASTA

>9P6E_4 RM20A3 light chain (chains I, M, Q)
ALTQPPSVSGSPGQSVTISCTGTSSDIGSYNYVSWYQQHPGKAPKLMIYDVTQRPSGVSD
RFSGSKSGNTASLTISGLQADDEADYYCSAYAGRQTFYIFGGGTRLTVL

Sequence of entity 5 (H, K, P), FASTA

>9P6E_5 N49P7-FR heavy chain (chains H, K, P)
ADLVQSGAVVKKPGDSVRISCEAQGYRFPDYIIHWIRRAPGQGPEWMGWMNPMGGQVNIP
WKFQGRVSMTRQLSQDPDDPDWGTAFLDLRGLKSDDTAVYYCVRDRSNGSGKRFESSNWF
LDLWGRGTAVTIQS

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

>9P6E_6 N49P7-FR light chain (chains L, N, R)
QSALTQPRSVSASPGQSVTISCTGTHNLVSWCQHQPGRAPKLLIYDFNKRPSGVPDRFSG
SGSGGTASLTITGLQDDDDAEYFCWAYEAFGGGTKLTVL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	33

Primary citation

Engineering HIV antibodies with enhanced breadth and potency of neutralization through multistate affinity maturation. Kedzior, M., Phulera, S., Fernandez-Quintero, M.L. et al. bioRxiv (2025). DOI 10.1101/2025.10.22.684031 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S5), best resolution first:

6CDO 2.1 Å, Structure of vaccine-elicited HIV-1 neutralizing antibody vFP16.02 in complex with HIV-1…
6CDM 2.41 Å, Structure of vaccine-elicited HIV-1 neutralizing antibody vFP7.04 in complex with HIV-1…
6CDP 2.46 Å, Vaccine-elicited HIV-1 neutralizing antibody vFP20.01 in complex with HIV-1 fusion…
9P6G 2.7 Å, eN49P7-FRv1-23 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
8TTW 2.96 Å, Cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with temsavir, 8ANC195,…
9Y9V 2.98 Å, The cryoem structure of rhesus macaque 1A8 and PGT121 fabs in complex with BG505…
9Q0W 3.0 Å, Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab
9Q3S 3.01 Å, Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env…
5U7M 3.02 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
5U7O 3.03 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
4TVP 3.1 Å, Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising…
8TKC 3.1 Å, cryo-EM structure of HIV-1 BG505DS-SOSIP.664 env trimer bound to DJ85-b.01 FAB

Browse structure collections

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