8FK5: PG9RSH DU011 Fab

Cryo-EM Structure of PG9RSH DU011 Fab in complex with BG505 DS-SOSIP.664. Determined by electron microscopy at 3.4 Å resolution. Released 31 May 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 8
Atoms: 16,980
Mol. weight: 286.47 kDa
Ligands: NAG
Released: 31 May 2023

Explore 8FK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FK5 contains 65 α-helices and 152 β-strands across 8 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: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	524-527	4
α-helix	530-534	5
α-helix	537-541	5
α-helix	570-595	26
β-strand	603-609	7	1
α-helix	619-624	6
α-helix	628-635	8
α-helix	639-663	25

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	524-526	3
α-helix	532-536	5
α-helix	537-542	6
α-helix	572-595	24
β-strand	603-609	7	2
α-helix	620-623	4
α-helix	628-634	7
α-helix	639-663	25

Chain C: 14 helices, 38 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	58-63	6
β-strand	75-76	2	4
α-helix	77-78	2
β-strand	84-86	3	3
β-strand	91-94	4	5
α-helix	100-114	15
β-strand	121-122	2	6
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
α-helix	194-197	4
β-strand	201-202	2	6
β-strand	203	1	9
β-strand	215	1	10
β-strand	216-218	3	4
β-strand	223-228	6	3
β-strand	236-239	4	5
β-strand	242-245	4	3
β-strand	247	1	4
α-helix	248-250	3
β-strand	251	1	10
α-helix	252	1
β-strand	260-261	2	11
α-helix	264-266	3
β-strand	271-273	3	11
β-strand	284-309	26	11
β-strand	315-323	10	11
β-strand	326	1	8
β-strand	329-333	5	11
α-helix	335-352	18
β-strand	358-361	4	11
α-helix	369-372	4
β-strand	374-378	5	11
β-strand	381-385	5	11
α-helix	387-389	3
β-strand	393-395	3	11
β-strand	414-420	7	11
β-strand	435	1	9
α-helix	436-440	5
β-strand	441-456	16	11
β-strand	465-470	6	11
α-helix	477-483	7
β-strand	486-491	6	3
β-strand	494-499	6	1

Chain F: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-542	6
α-helix	573-594	22
β-strand	603-609	7	12
α-helix	619-621	3
α-helix	628-635	8
α-helix	639-661	23

Chain G: 17 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	2
β-strand	45-47	3	13
α-helix	52	1
β-strand	53-56	4	14
α-helix	58-61	4
β-strand	75-76	2	14
β-strand	83-86	4	13
β-strand	91-94	4	15
α-helix	99-114	16
α-helix	120	1
β-strand	121	1	16
α-helix	123-125	3
β-strand	129-133	5	17
α-helix	140-150	3
β-strand	154-162	9	17
β-strand	169-177	9	17
α-helix	178-180	3
β-strand	181-183	3	17
β-strand	190-193	4	17
α-helix	194-197	4
β-strand	202-203	2	16
α-helix	204-205	2
β-strand	215	1	18
β-strand	216-218	3	14
β-strand	223-228	6	13
β-strand	236-239	4	15
β-strand	242-245	4	13
α-helix	248-250	3
β-strand	251	1	18
β-strand	259-260	2	19
α-helix	264-266	3
β-strand	271-273	3	19
β-strand	284-287	4	19
β-strand	294-298	5	20
β-strand	301	1	21
β-strand	304-312	7	22
β-strand	315-320	6	22
α-helix	321A-322	2
β-strand	323	1	21
β-strand	329-334	6	20
α-helix	335-349	15
α-helix	350-352	3
β-strand	358-361	4	19
α-helix	369-372	4
β-strand	374-378	5	20
β-strand	381-385	5	20
α-helix	387-389	3
β-strand	393-395	3	19
β-strand	413-420	8	20
β-strand	423-424	2	16
β-strand	434-435	2	16
β-strand	443-447	5	20
β-strand	451-457	7	19
β-strand	465-470	6	19
α-helix	475-483	9
β-strand	486-491	6	13
β-strand	494-499	6	2

Chain H: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	35
β-strand	10-12	3	36
β-strand	17-25	9	35
β-strand	34-39	6	36
β-strand	46-51	6	36
β-strand	57-59	3	36
α-helix	61-63	3
β-strand	67-72	6	35
β-strand	77-82A	7	35
α-helix	84-86	3
β-strand	88-98	11	36
β-strand	100-100B	3	29
β-strand	100E-100J	6	29
α-helix	100M-100N	2
β-strand	100O-103	9	36
β-strand	107-111	5	36

Chain I: 9 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	12
β-strand	45-47	3	23
β-strand	53-56	4	24
α-helix	58-62	5
β-strand	67	1	25
β-strand	75-76	2	24
β-strand	84-86	3	23
β-strand	91-94	4	26
α-helix	99-114	16
β-strand	121	1	27
β-strand	129	1	28
β-strand	130-133	4	29
β-strand	138	1	30
β-strand	154-162	9	29
β-strand	168-177	10	29
α-helix	178-180	3
β-strand	181-183	3	28
β-strand	191-193	3	28
α-helix	194-197	4
β-strand	202-203	2	27
α-helix	204-205	2
β-strand	209	1	25
β-strand	215	1	31
β-strand	216-218	3	24
β-strand	223-228	6	23
β-strand	236-239	4	26
β-strand	242-245	4	23
β-strand	247	1	24
β-strand	251	1	31
β-strand	259-261	3	32
β-strand	271-273	3	32
β-strand	284-292	9	32
β-strand	294-298	5	33
β-strand	301-312	10	34
β-strand	315-323	10	34
β-strand	326	1	30
β-strand	329-333	5	33
α-helix	335-353	19
β-strand	359-361	3	32
α-helix	369-372	4
β-strand	374-378	5	33
β-strand	381-385	5	33
β-strand	393-395	3	32
β-strand	414-421	8	33
β-strand	423-424	2	27
β-strand	434-435	2	27
α-helix	436-438	3
β-strand	443-446	4	33
β-strand	449-456	8	32
β-strand	466-470	5	32
α-helix	476-480	5
β-strand	486-491	6	23
β-strand	494-499	6	12

Chain L: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4	1	37
β-strand	5	1	38
β-strand	9-13	4	39
β-strand	19-24	6	38
β-strand	33-38	6	39
β-strand	45-48	4	39
β-strand	50	1	40
β-strand	53	1	40
β-strand	62-67	6	38
β-strand	70-75	6	38
α-helix	80-82	3
β-strand	84-91	8	39
β-strand	96-98	3	39
β-strand	99	1	37
β-strand	102-106	5	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp41	A, B, F	protein	153	Human immunodeficiency virus 1	Q2N0S6
Envelope glycoprotein gp120	C, G, I	protein	481	Human immunodeficiency virus 1	Q2N0S6
Immunoblobulin G1 Fab heavy chain variable region (Fragment)	H	protein	248	Homo sapiens	A4F255 (AlphaFold model)
Immunoglobulin lambda-1 light chain-like	L	protein	216	Homo sapiens	Q6PJG0 (AlphaFold model)

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

>8FK5_1 Envelope glycoprotein gp41 (chains A, B, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>8FK5_2 Envelope glycoprotein gp120 (chains C, G, I)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 3 (H), FASTA

>8FK5_3 Immunoblobulin G1 Fab heavy chain variable region (Fragment) (chains H)
ERLVESGGGVVQPGSSLRLSCAASGFDFSRQGMHWVRQAPGQGLEWVAFIKYDGSEKYHA
DSVWGRLSISRDNSKDTLYLQMNSLRVEDTATYFCVREAGGPDYRNGYYYYDFYDGYYNY
HYMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSG
ALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD
KGLEVLFQ

Sequence of entity 4 (L), FASTA

>8FK5_4 Immunoglobulin lambda-1 light chain-like (chains L)
QSALTQPASVSGSPGQSITISCQGTSNDVGGYESVSWYQQHPGKAPKVVIYDVSKRPSGV
SNRFSGSKSGNTASLTISGLQAEDEGDYYCKSLTSRSHRVFGTGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	38

Primary citation

Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design. Holt, G.T., Gorman, J., Wang, S. et al. Cell Rep (2023) 42:112711-112711. DOI 10.1016/j.celrep.2023.112711 · 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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