8DOK: T/F100 SOSIP.664 HIV-1 Env trimer

Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 and 10-1074. Determined by electron microscopy at 3.2 Å resolution. Released 19 Jul 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 18
Atoms: 25,844
Mol. weight: 533.68 kDa
Ligands: NAG
Released: 19 Jul 2023

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

Secondary structure: helices and β-sheets

8DOK contains 76 α-helices and 266 β-strands across 18 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: 15 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
α-helix	51-52	2
β-strand	53-55	3	3
β-strand	56	1	4
β-strand	67	1	5
β-strand	77	1	4
β-strand	83-85	3	2
β-strand	89	1	6
β-strand	91-94	4	7
α-helix	95-97	3
α-helix	100-116	17
α-helix	120	1
β-strand	121	1	8
α-helix	123-125	3
β-strand	129-131	3	9
β-strand	154-162	9	9
β-strand	169-177	9	9
α-helix	178-180	3
β-strand	181-183	3	9
β-strand	190-193	4	9
β-strand	202-203	2	8
α-helix	204-205	2
β-strand	209	1	5
β-strand	215	1	10
β-strand	216-218	3	3
β-strand	223-227	5	2
β-strand	236-239	4	7
β-strand	241	1	6
β-strand	243-245	3	2
β-strand	247	1	3
β-strand	251	1	10
β-strand	259-261	3	11
α-helix	264-266	3
β-strand	271-274	4	11
α-helix	283	1
β-strand	284-298	15	11
β-strand	302-312	9	12
β-strand	315-322	9	12
β-strand	329-334	6	11
α-helix	335-352	18
α-helix	356	1
β-strand	357-361	4	11
α-helix	369-372	4
β-strand	374-377	4	11
β-strand	382-385	4	11
β-strand	393-395	3	11
β-strand	413-418	6	11
β-strand	421	1	11
β-strand	423-424	2	8
α-helix	432-433	2
β-strand	434-435	2	8
α-helix	437-439	3
β-strand	443-457	15	11
β-strand	465-470	6	11
α-helix	475-478	4
β-strand	486-491	6	2
β-strand	494-499	6	1

Chain B: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-540	11
α-helix	570-595	26
β-strand	603-609	7	1
α-helix	619-623	5
α-helix	628-634	7
α-helix	639-661	23

Chain C: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
β-strand	10-11	2	14
β-strand	18-25	8	13
β-strand	33-39	8	15
β-strand	45-52	8	15
β-strand	57-59	3	15
α-helix	61-63	3
β-strand	67-72	6	13
β-strand	77D-82	6	13
α-helix	84-86	3
β-strand	89-96	8	15
β-strand	100E-100F	2	16
β-strand	100I-100J	2	16
β-strand	102-103	2	15
β-strand	107-108	2	15
β-strand	109-110	2	14

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	17
β-strand	10-12	3	18
β-strand	19-25	7	17
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	85-90	6	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-105	4	18

Chain E: 10 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	19
β-strand	45-47	3	20
β-strand	53-55	3	21
α-helix	61-64	4
β-strand	67	1	22
α-helix	75-77	3
β-strand	83-85	3	20
β-strand	91-94	4	23
α-helix	95-97	3
α-helix	100-114	15
β-strand	121	1	24
α-helix	123-125	3
β-strand	129-131	3	25
β-strand	154-162	9	25
β-strand	169-177	9	25
β-strand	181-183	3	25
β-strand	190-193	4	25
β-strand	202-203	2	24
α-helix	204-205	2
β-strand	209	1	22
β-strand	215	1	26
β-strand	216-218	3	21
β-strand	223-227	5	20
β-strand	236-239	4	23
β-strand	243-245	3	20
β-strand	247	1	21
β-strand	251	1	26
β-strand	259-261	3	27
β-strand	271-273	3	27
β-strand	284-298	15	27
β-strand	304-312	7	28
β-strand	315-320	6	28
β-strand	329-334	6	27
α-helix	335-352	18
β-strand	357-361	4	27
α-helix	369-372	4
β-strand	374-377	4	27
β-strand	382-385	4	27
β-strand	394-395	2	27
β-strand	413-421	9	27
β-strand	423-424	2	24
β-strand	434-435	2	24
α-helix	437-439	3
β-strand	443-456	14	27
β-strand	465-470	6	27
α-helix	475-479	5
β-strand	486-491	6	20
β-strand	494-499	6	19

Chain F: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-535	6
α-helix	570-595	26
β-strand	603-609	7	19
α-helix	619-624	6
α-helix	628-634	7
α-helix	639-660	22

Chain G: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	29
β-strand	10-11	2	30
β-strand	18-25	8	29
β-strand	33-39	8	31
β-strand	45-52	8	31
β-strand	56-59	4	31
β-strand	67-72	6	29
β-strand	77D-82	6	29
α-helix	84-86	3
β-strand	89-96	8	31
β-strand	100E-100F	2	32
β-strand	100I-100J	2	32
β-strand	102-103	2	31
β-strand	107-108	2	31
β-strand	109-110	2	30

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	33
β-strand	10-12	3	34
β-strand	18-25	8	33
β-strand	33-38	6	34
β-strand	45-49	5	34
β-strand	53-54	2	34
α-helix	55	1
β-strand	62-67	6	33
β-strand	70-76	7	33
β-strand	85-90	6	34
α-helix	96	1
β-strand	97-98	2	34
β-strand	102-105	4	34

10 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRF-1_AE T/F100 Env gp120	A, E, I	protein	486	Human immunodeficiency virus 1	A0A140EMT3
CRF-1_AE T/F100 HIV-1 gp41	B, F, J	protein	155	Human immunodeficiency virus 1	A0A140EMT3
Heavy chain of 8ANC195	C, G, K	protein	238	Homo sapiens	P01857 (AlphaFold model)
Light chain of 8ANC195	D, H, L	protein	215	Homo sapiens	P01834 (AlphaFold model)
Heavy chain of 10-1074	M, O, Q	protein	238	Homo sapiens	P01857 (AlphaFold model)
Light chain of 10-1074	N, P, R	protein	214	Homo sapiens	P0DOY2 (AlphaFold model)

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

>8DOK_1 CRF-1_AE 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

>8DOK_2 CRF-1_AE T/F100 HIV-1 gp41 (chains B, F, J)
AVGLGAMIFGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAPEAQQHLLQLTVW
GIKQLQARVLAVERYLQDQKFLGLWGCSGKIICCTAVPWNSSWSNKTFEEIWNNMTWIEW
EREISNYTSQIYDILTISQTQQEKNEKDLLELDAA

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

>8DOK_3 Heavy chain of 8ANC195 (chains C, G, K)
QIHLVQSGTEVKKPGSSVTVSCKAYGVNTFGLYAVNWVRQAPGQSLEYIGQIWRWKSSAS
HHFRGRVLISAVDLTGSSPPISSLEIKNLTSDDTAVYFCTTTSTYDRWSGLHHDGVMAFS
SWGQGTLISVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKT

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

>8DOK_4 Light chain of 8ANC195 (chains D, H, L)
DIQMTQSPSTLSASTGDTVRISCRASQSITGNWVAWYQQRPGKAPRLLIYRGAALLGGVP
SRFRGSAAGTDFTLTIGNLQAEDFGTFYCQQYDTYPGTFGQGTKVEVKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (M, O, Q), FASTA

>8DOK_5 Heavy chain of 10-1074 (chains M, O, Q)
QVQLQESGPGLVKPSETLSVTCSVSGDSMNNYYWTWIRQSPGKGLEWIGYISDRESATYN
PSLNSRVVISRDTSKNQLSLKLNSVTPADTAVYYCATARRGQRIYGVVSFGEFFYYYSMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKT

Sequence of entity 6 (N, P, R), FASTA

>8DOK_6 Light chain of 10-1074 (chains N, P, R)
SYVRPLSVALGETARISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERFSGT
PDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	42

Primary citation

Structure-function analyses reveal key molecular determinants of HIV-1 CRF01_AE resistance to the entry inhibitor temsavir. Prevost, J., Chen, Y., Zhou, F. et al. Nat Commun (2023) 14:6710-6710. DOI 10.1038/s41467-023-42500-2 · 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…
6NQD 3.9 Å, Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab

Browse structure collections

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