6U59: HIV-1 B41 SOSIP.664

HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B. Determined by electron microscopy at 3.86 Å resolution. Released 29 Jan 2020.

Method: Electron microscopy
Resolution: 3.86 Å
Organisms: Human immunodeficiency virus 1, Oryctolagus cuniculus
Chains: 12
Atoms: 20,439
Mol. weight: 327.64 kDa
Ligands: NAG
Released: 29 Jan 2020

Explore 6U59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U59 contains 78 α-helices and 189 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, C and G: 13 helices, 37 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	75	1	3
α-helix	76-78	3
β-strand	84-85	2	2
β-strand	91-94	4	4
α-helix	95-97	3
α-helix	99-115	17
α-helix	123-125	3
β-strand	129-132	4	5
β-strand	155-162	8	5
β-strand	169-176	8	5
α-helix	178-180	3
β-strand	181-183	3	5
β-strand	190-193	4	5
β-strand	201-203	3	6
α-helix	204-205	2
β-strand	215-218	4	3
α-helix	219-220	2
β-strand	221	1	2
β-strand	223-228	6	2
β-strand	236-239	4	4
β-strand	242-245	4	2
β-strand	247-251	5	3
β-strand	257	1	7
β-strand	259-261	3	7
α-helix	264-266	3
β-strand	271-273	3	7
α-helix	283	1
β-strand	284-298	15	7
β-strand	301-312	10	8
β-strand	315-323A	10	8
β-strand	329-334	6	7
α-helix	335-352	18
β-strand	357-361	4	9
β-strand	374-378	5	7
β-strand	381-385	5	7
α-helix	388-390	3
β-strand	394-395	2	9
β-strand	413-421	9	7
β-strand	423-424	2	6
β-strand	433-435	3	6
α-helix	436-438	3
β-strand	443-454	12	7
β-strand	455-456	2	9
β-strand	465-469	5	9
α-helix	476-483	8
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains B, D and I: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	526-529	4
α-helix	539-542	4
α-helix	570-596	27
β-strand	603-604	2	1
β-strand	609	1	1
α-helix	619-622	4
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-647	9
α-helix	652-661	10

Chains E, J and L: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	11-13	3	25
β-strand	19-25	7	24
α-helix	30-32	3
β-strand	33-38	6	25
β-strand	45-50	6	25
β-strand	53-54	2	25
α-helix	55	1
β-strand	63-67	5	24
β-strand	70-75	6	24
α-helix	80-82	3
β-strand	84-90	7	25
β-strand	93	1	26
β-strand	97-98	2	25
β-strand	102-106	5	25

Chains F, H and K: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	27
β-strand	10-12	3	28
β-strand	18-23	6	27
β-strand	32-39	8	28
α-helix	45	1
β-strand	46-51	6	28
β-strand	57-59	3	28
β-strand	67-73	7	27
β-strand	76-81	6	27
α-helix	84-86	3
β-strand	88-96	9	28
β-strand	100C	1	26
β-strand	100G-101	2	28
β-strand	107-111	5	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SOSIP.664 gp120,SOSIP.664 gp120	A, C, G	protein	524	Human immunodeficiency virus 1	B3UES2
SOSIP.664 gp41	B, D, I	protein	153	Human immunodeficiency virus 1	B3UEZ6
rabbit antibody 13B Fragment antigen binding light chain	E, J, L	protein	112	Oryctolagus cuniculus
rabbit antibody 13B Fragment antigen binding heavy chain	F, H, K	protein	119	Oryctolagus cuniculus

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

>6U59_1 SOSIP.664 gp120,SOSIP.664 gp120 (chains A, C, G)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRVVQRRRRRR

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

>6U59_2 SOSIP.664 gp41 (chains B, D, I)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 3 (E, J, L), FASTA

>6U59_3 rabbit antibody 13B Fragment antigen binding light chain (chains E, J, L)
DIVMTQTPASVSEPVGGTVTINCQASQSRGNNYLSWYQQKPGQSPSLLIYRTSTLASGVP
SRFKGSGSGTQFTLTISDLECADAATYYCLYGYYSSRNPDFAFGGGTEVVVK

Sequence of entity 4 (F, H, K), FASTA

>6U59_4 rabbit antibody 13B Fragment antigen binding heavy chain (chains F, H, K)
LEESGGGLVQPEGSLTLTCKASGFDFSDYHVQWVRQSPGKGLEFIGGIAYTGNIYYASWA
KGRFTISKTSSTTVTLQMTTLTAADTATYFCARAYGYASAPYAQYFNLWGPGTLVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	30

Primary citation

Autologous Antibody Responses to an HIV Envelope Glycan Hole Are Not Easily Broadened in Rabbits. Yang, Y.R., McCoy, L.E., van Gils, M.J. et al. J Virol (2020) 94. DOI 10.1128/JVI.01861-19 · PubMed

Other PDB entries of the same protein (UniProt B3UES2), best resolution first:

6MUF 2.91 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human…
6MUG 2.95 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6OKP 3.28 Å, B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody…
6OPN 3.5 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35
6OPO 3.5 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
6MCO 3.53 Å, Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P23…
5VN8 3.6 Å, Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain…
6X5B 3.6 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule…
5VN3 3.7 Å, Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen…
6OPP 3.7 Å, Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
6OPQ 3.8 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG
6MDT 3.82 Å, Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63…

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