8T4K: MD64 N332-GT5 sosip

MD64 N332-GT5 sosip. Determined by electron microscopy at 2.6 Å resolution. Released 8 May 2024.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Human immunodeficiency virus 1
Chains: 6
Atoms: 13,560
Mol. weight: 226.04 kDa
Ligands: NAG
Released: 8 May 2024

Explore 8T4K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T4K contains 69 α-helices and 123 β-strands across 6 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 D: 13 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53-56	4	3
β-strand	67	1	4
β-strand	75-76	2	3
β-strand	84-86	3	2
β-strand	91-94	4	5
α-helix	99-115	17
α-helix	123-125	3
β-strand	129-133	5	6
β-strand	154-162	9	6
β-strand	169-177	9	6
α-helix	178-180	3
β-strand	181-183	3	6
β-strand	189-193	5	6
α-helix	194-197	4
β-strand	200-203	4	7
α-helix	204-205	2
β-strand	209	1	4
β-strand	215	1	8
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
α-helix	248-250	3
β-strand	251	1	8
β-strand	256	1	6
β-strand	259-261	3	6
α-helix	264-266	3
β-strand	271-274	4	6
β-strand	284-312	27	6
β-strand	315-323A	10	6
β-strand	329-334	6	6
α-helix	335-353	19
β-strand	358-361	4	6
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
β-strand	393-395	3	6
β-strand	413-421	9	6
β-strand	423-424	2	7
α-helix	426-428	3
β-strand	432-435	4	7
α-helix	437-439	3
β-strand	441-456	16	6
β-strand	465-470	6	6
α-helix	476-483	8
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains B, E and F: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	524-527	4
β-strand	529	1	9
α-helix	530-533	4
α-helix	537-541	5
α-helix	572-595	24
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	619-620	2
α-helix	621-625	5
β-strand	627	1	9
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-661	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MD64 N332-GT5 SOSIP gp120	A, C, D	protein	481	Human immunodeficiency virus 1	Q2N0S6
MD64 N332-GT5 SOSIP gp41	B, E, F	protein	162	Human immunodeficiency virus 1	Q2N0S8

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

>8T4K_1 MD64 N332-GT5 SOSIP gp120 (chains A, C, D)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPKLRSMMRGEIKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
IIRSENITNNAKNILVQLNTPVQINCTRPSNNTVKSIRIGPGQAFYYFGDVLGHVRMAHC
NISKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSLILPCWIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

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

>8T4K_2 MD64 N332-GT5 SOSIP gp41 (chains B, E, F)
AVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHW
GIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALDGTKHHHHHH

Ligands and cofactors

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

Primary citation

Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates. Steichen, J.M., Phung, I., Salcedo, E. et al. Science (2024) 384:eadj8321-eadj8321. DOI 10.1126/science.adj8321 · 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
8EUU 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB
8EUW 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-MM28 FAB

Browse structure collections

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