5VN8: Cryo-EM model of B41 SOSIP.664

Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12. Determined by electron microscopy at 3.6 Å resolution. Released 12 Jul 2017.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,589
Mol. weight: 394.77 kDa
Ligands: NAG
Released: 12 Jul 2017

Explore 5VN8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VN8 contains 70 α-helices and 204 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 C: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	526	1	15
β-strand	528	1	15
β-strand	529	1	16
α-helix	530-545	16
α-helix	566-569	4
α-helix	571-592	22
α-helix	593-595	3
β-strand	603	1	1
α-helix	608	1
β-strand	609	1	1
α-helix	610-611	2
α-helix	620-625	6
β-strand	627	1	16
α-helix	628-632	5
α-helix	639-662	24

Chains D and E: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	23
β-strand	45-47	3	24
β-strand	53	1	25
β-strand	55	1	26
β-strand	75	1	26
α-helix	76-78	3
β-strand	83-85	3	24
β-strand	93-94	2	27
α-helix	101-105	5
α-helix	110-114	5
β-strand	181	1	28
β-strand	184	1	29
α-helix	185F-185H	3
β-strand	190	1	29
β-strand	193	1	28
β-strand	201	1	30
β-strand	215	1	31
β-strand	218	1	25
β-strand	223-228	6	24
β-strand	236-237	2	27
β-strand	242-245	4	24
β-strand	251	1	31
β-strand	259-261	3	32
β-strand	271-273	3	32
β-strand	284-302	19	32
β-strand	330-333	4	32
α-helix	335-352	18
β-strand	357-361	4	33
α-helix	369-372	4
β-strand	374-375	2	34
β-strand	378	1	35
β-strand	381	1	35
β-strand	383-385	3	34
β-strand	414-417	4	32
β-strand	418-420	3	34
β-strand	423-424	2	36
β-strand	433	1	30
β-strand	434-435	2	36
α-helix	436-438	3
β-strand	441-454	14	32
β-strand	455-456	2	33
β-strand	465-469	5	33
α-helix	477-480	4
β-strand	486-491	6	24
β-strand	494-499	6	23

Chains F, H and I: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	39
β-strand	20-21	2	40
β-strand	24	1	39
α-helix	29-31	3
β-strand	34-39	6	41
β-strand	45-52	8	41
β-strand	56-58	3	41
α-helix	61-63	3
β-strand	67-72	6	40
β-strand	77-82	6	40
α-helix	84-86	3
β-strand	89-90	2	41
β-strand	93-94	2	41
α-helix	95-99	5
β-strand	102	1	41
β-strand	104	1	39
β-strand	107-108	2	41

Chain G: 9 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53	1	3
β-strand	55	1	4
β-strand	75	1	4
α-helix	76-78	3
β-strand	83-85	3	2
α-helix	91-92	2
β-strand	93-94	2	5
α-helix	101-105	5
α-helix	110-114	5
β-strand	181	1	6
β-strand	184	1	7
α-helix	185F-185H	3
β-strand	190	1	7
β-strand	193	1	6
β-strand	201	1	8
β-strand	215	1	9
β-strand	218	1	3
β-strand	223-228	6	2
β-strand	236-237	2	5
β-strand	242-245	4	2
β-strand	251	1	9
β-strand	259-261	3	10
β-strand	271-273	3	10
β-strand	284-302	19	10
β-strand	330-333	4	10
α-helix	335-352	18
β-strand	357-361	4	11
α-helix	369-372	4
β-strand	374-375	2	12
β-strand	378	1	13
β-strand	381	1	13
β-strand	383-385	3	12
β-strand	414-417	4	10
β-strand	418-420	3	12
β-strand	423-424	2	14
β-strand	433	1	8
β-strand	434-435	2	14
α-helix	436-438	3
β-strand	441-454	14	10
β-strand	455-456	2	11
β-strand	465-469	5	11
α-helix	477-480	4
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains J, K and L: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	42
β-strand	18	1	43
β-strand	21-25	5	42
β-strand	35-38	4	41
β-strand	44-48	5	41
β-strand	54	1	41
α-helix	55	1
β-strand	62-65	4	42
β-strand	71-75	5	42
β-strand	76	1	43
α-helix	80-82	3
β-strand	85-86	2	41
β-strand	88	1	41
β-strand	102-103	2	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	D, E, G	protein	516	Human immunodeficiency virus 1	B3UES2
Envelope glycoprotein gp160	A, B, C	protein	153	Human immunodeficiency virus 1	B3UEZ6
b12 Fab heavy chain	F, H, I	protein	230	Homo sapiens
b12 Fab light chain	J, K, L	protein	215	Homo sapiens

Sequence of entity 1 (D, E, G), FASTA

>5VN8_1 Envelope glycoprotein gp160 (chains D, E, G)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV

Sequence of entity 2 (A, B, C), FASTA

>5VN8_2 Envelope glycoprotein gp160 (chains A, B, C)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 3 (F, H, I), FASTA

>5VN8_3 b12 Fab heavy chain (chains F, H, I)
QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEF
SAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKG
TTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC

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

>5VN8_4 b12 Fab light chain (chains J, K, L)
EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGIS
DRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Ozorowski, G., Pallesen, J., de Val, N. et al. Nature (2017) 547:360-363. DOI 10.1038/nature23010 · 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…
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…
6U59 3.86 Å, HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B

Browse structure collections

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