6NQD: T/F100 SOSIP.664 HIV-1 Env trimer

Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab. Determined by electron microscopy at 3.9 Å resolution. Released 6 Mar 2019.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,175
Mol. weight: 402 kDa
Ligands: NAG
Released: 6 Mar 2019

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

Secondary structure: helices and β-sheets

6NQD contains 45 α-helices and 207 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, E and I: 8 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-46	2	2
β-strand	53-55	3	3
β-strand	56	1	4
β-strand	77	1	4
β-strand	84	1	2
β-strand	93-94	2	5
α-helix	95-97	3
α-helix	100-113	14
β-strand	129-131	3	6
β-strand	157-162	6	6
β-strand	169-174	6	6
β-strand	181-183	3	6
β-strand	189-193	5	6
α-helix	200-201	2
β-strand	203	1	7
β-strand	215	1	8
β-strand	216-218	3	3
β-strand	223-227	5	2
β-strand	236-237	2	5
β-strand	243-245	3	2
β-strand	247	1	3
β-strand	251	1	8
β-strand	261	1	9
α-helix	264-266	3
β-strand	271-273	3	9
α-helix	283	1
β-strand	284-298	15	9
β-strand	300-312	11	10
β-strand	315-324	11	10
β-strand	329-334	6	9
α-helix	335-352	18
β-strand	358-361	3	11
β-strand	374-375	2	9
β-strand	382-385	4	9
α-helix	388-390	3
β-strand	393-395	3	11
β-strand	413-421	9	9
β-strand	423-424	2	7
β-strand	434-435	2	7
β-strand	443-454	12	9
β-strand	455	1	12
β-strand	466-467	2	11
β-strand	469	1	12
α-helix	477-480	4
β-strand	488-491	4	2
β-strand	494-496	3	1
β-strand	499	1	1

Chains B, F and J: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-547	18
α-helix	573-592	20
β-strand	604-609	6	1
α-helix	619-623	5
α-helix	628-634	7
α-helix	639-659	21

Chains C, G and K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	13
β-strand	17-25	9	13
β-strand	34-39	7	14
α-helix	44	1
β-strand	45-52	8	14
β-strand	58-59	2	14
β-strand	67-72	6	13
β-strand	77D-82A	7	13
β-strand	88-95	8	14
β-strand	100E-100F	2	15
β-strand	100I-100J	2	15
β-strand	102	1	14
β-strand	107-109	3	14

Chains D, H and L: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	16
β-strand	10-12	3	17
β-strand	18-24	7	16
β-strand	33	1	18
β-strand	34-38	5	17
β-strand	40	1	19
β-strand	42	1	19
β-strand	45-49	5	17
β-strand	53-54	2	17
β-strand	62-67	6	16
β-strand	70-76	7	16
α-helix	80-82	3
β-strand	84-87	4	17
β-strand	89	1	20
β-strand	90	1	18
β-strand	98	1	20
β-strand	102-105	4	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T/F100 Env gp120	A, E, I	protein	486	Human immunodeficiency virus 1	A0A140EMT3
T/F100 Env gp41	B, F, J	protein	184	Human immunodeficiency virus 1	A0A140EMT3
8ANC195 G52K5 heavy chain, IG gamma-1 chain	C, G, K	protein	244	Homo sapiens	S6B2A6 (AlphaFold model)
8ANC195 G52K5 light chain	D, H, L	protein	215	Homo sapiens	P0DOX7 (AlphaFold model)

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

>6NQD_1 T/F100 Env gp120 (chains A, E, I)
ATNNLWVTVYYGVPVWRDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEMHLKNV
TENFNMWKNNMVEQMQEDVISLWDQSLKPCVKLTPLCVTLNCTSATVTNYTKVNDTSDII
GNITDDVRNCSFNMTTELRDKQQKVYALFYKLDIVPIDDSSNNGSSNFSEYRLINCNTSV
IKQACPKVSFDPIPIHYCTPAGYAILRCNDKKFNGTGPCKNVSSVQCTHGIKPVVSTQLL
LNGSLAEEGIIIRSENLTNNAKTIIVHFNESVKINCTRPSNNTRTGIHIGPGQVFYKTGD
IIGDIRKAYCNISGAQWHKVLGRVANKLKEHFNNKTIVFKPSSGGDPEITMHHFNCRGEF
FYCNTTKLFNSTWGGNKNETRDNGTITIPCRIKQIINMWQGVGQAMYAPPIKGVIKCLSN
ITGILLTRDGGNDSTENNETFRPGGGNIKDNWRNELYKYKVVQIEPLGIAPTKCKRRVVE
RRRRRR

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

>6NQD_2 T/F100 Env gp41 (chains B, F, J)
AVGLGAMIFGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAPEAQQHLLQLTVW
GIKQLQARVLAVERYLQDQKFLGLWGCSGKIICCTAVPWNSSWSNKTFEEIWNNMTWIEW
EREISNYTSQIYDILTISQTQQEKNEKDLLELDAAAWSHPQFEKGGGSGGGSGGSAWSHP
QFEK

Sequence of entity 3 (C, G, K), FASTA

>6NQD_3 8ANC195 G52K5 heavy chain, IG gamma-1 chain (chains C, G, K)
QIHLVQSGTEVKKPGSSVTVSCKAYGVNTFGLYAVNWVRQAPGQSLEYIGQIWRWKSSAS
HHFRGRVLISAVDLTGSSPPISSLEIKNLTSDDTAVYFCTTTSTYDRWSGLHHDGVMAFS
SWGQGTLISVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHH
HHHH

Sequence of entity 4 (D, H, L), FASTA

>6NQD_4 8ANC195 G52K5 light chain (chains D, H, L)
DIQMTQSPSTLSASTGDTVRISCRASQSITGNWVAWYQQRPGKAPRLLIYRGAALLGGVP
SRFRGSAAGTDFTLTIGNLQAEDFGTFYCQQYDTYPGTFGQGTKVEVKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

A sequestered fusion peptide in the structure of an HIV-1 transmitted founder envelope trimer. Ananthaswamy, N., Fang, Q., AlSalmi, W. et al. Nat Commun (2019) 10:873-873. DOI 10.1038/s41467-019-08825-7 · PubMed

Other PDB entries of the same protein (UniProt A0A140EMT3), best resolution first:

8CZZ 3.14 Å, Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex…
8DOK 3.2 Å, Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 and 10-1074

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