8DOW: HIV-1 Env(CH848 10.17 DS.SOSIP_DT)

Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab. Determined by electron microscopy at 3.69 Å resolution. Released 19 Jul 2023.

Method: Electron microscopy
Resolution: 3.69 Å
Organisms: Human immunodeficiency virus 1, Macaca mulatta
Chains: 12
Atoms: 25,053
Mol. weight: 370.8 kDa
Ligands: NAG
Released: 19 Jul 2023

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

Secondary structure: helices and β-sheets

8DOW contains 125 α-helices and 269 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.

Chain A: 17 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	1
β-strand	45-47	3	2
β-strand	53-55	3	3
α-helix	63-66	4
β-strand	68	1	4
β-strand	75	1	3
α-helix	80-82	3
β-strand	84-85	2	2
β-strand	91-94	4	5
α-helix	100-116	17
β-strand	121	1	6
α-helix	123-125	3
β-strand	129-133	5	7
α-helix	139-150	4
β-strand	152-160	9	7
β-strand	167-175	9	7
α-helix	176-178	3
β-strand	179-181	3	7
β-strand	190-193	4	7
α-helix	200-201	2
β-strand	202-203	2	6
α-helix	204-205	2
β-strand	209	1	4
α-helix	213-214	2
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
β-strand	251	1	8
β-strand	257	1	9
β-strand	261	1	10
α-helix	263-266	4
β-strand	271-273	3	11
β-strand	284-287	4	11
β-strand	293-308	16	7
β-strand	316-323	9	7
β-strand	330-334	5	7
α-helix	335-352	18
β-strand	357-361	4	11
α-helix	369-372	4
β-strand	373-375	3	9
α-helix	378-380	3
β-strand	382-386	5	9
β-strand	394-395	2	11
β-strand	413-417	5	7
β-strand	418-421	4	9
β-strand	423-424	2	6
α-helix	426-428	3
β-strand	434-435	2	6
α-helix	436-438	3
β-strand	441-448	8	7
β-strand	449	1	10
β-strand	451-457	7	11
β-strand	465-470	6	11
α-helix	475-483	9
β-strand	486-491	6	2
β-strand	495-498	4	1

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-541	5
α-helix	570-596	27
β-strand	603-609	7	1
α-helix	612-614	3
α-helix	619-624	6
α-helix	628-635	8
α-helix	639-663	25

Chain C: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	32-39	8	13
β-strand	46-51	6	13
β-strand	58-60	3	13
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-101	10	13
β-strand	115	1	13
β-strand	119-123	5	13
β-strand	129	1	14
α-helix	130-131	2
β-strand	132-136	5	15
α-helix	140-144	5
β-strand	149-157	9	15
β-strand	158	1	14
β-strand	163-166	4	16
α-helix	167-169	3
β-strand	176-177	2	15
α-helix	178-180	3
β-strand	181-182	2	15
β-strand	188-195	8	15
α-helix	198-200	3
β-strand	201	1	17
β-strand	204	1	17
β-strand	207-212	6	16
β-strand	217-222	6	16

Chain D: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	18
β-strand	10-13	4	19
β-strand	19-25	7	18
β-strand	30	1	20
β-strand	36	1	20
β-strand	38-43	6	19
β-strand	50-54	5	19
β-strand	58-59	2	19
α-helix	60	1
β-strand	67-72	6	18
β-strand	75-80	6	18
α-helix	85-87	3
β-strand	89-95	7	19
α-helix	101	1
β-strand	102-103	2	19
β-strand	107-111	5	19
β-strand	116	1	21
α-helix	117-118	2
β-strand	119-123	5	22
α-helix	124	1
β-strand	125	1	15
α-helix	126	1
α-helix	127-131	5
β-strand	134-144	11	22
β-strand	145	1	21
β-strand	149-155	7	23
β-strand	158-159	2	23
β-strand	164-168	5	22
β-strand	178-187	10	22
α-helix	188-192	5
β-strand	196-203	8	23
β-strand	211-215	5	23

Chain E: 17 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	24
β-strand	45-47	3	25
β-strand	53-55	3	26
α-helix	63-66	4
β-strand	68	1	27
β-strand	75	1	26
α-helix	76	1
α-helix	80-82	3
β-strand	84-85	2	25
β-strand	91-94	4	28
α-helix	99-116	18
α-helix	120	1
β-strand	121	1	29
α-helix	123-125	3
β-strand	129-133	5	30
α-helix	139-150	4
β-strand	152-160	9	30
β-strand	167-175	9	30
α-helix	176-178	3
β-strand	179-181	3	30
β-strand	190-193	4	30
α-helix	201	1
β-strand	202-203	2	29
α-helix	204-205	2
β-strand	209	1	27
β-strand	215	1	31
β-strand	216-218	3	26
α-helix	219-220	2
β-strand	223-228	6	25
β-strand	236-239	4	28
β-strand	242-245	4	25
β-strand	247	1	26
β-strand	251	1	31
β-strand	261	1	32
α-helix	263-266	4
β-strand	271-273	3	33
β-strand	284-287	4	33
β-strand	293-308	16	30
β-strand	316-323	9	30
β-strand	330-334	5	30
α-helix	335-352	18
β-strand	357-361	4	33
α-helix	369-372	4
β-strand	373-375	3	34
β-strand	384-386	3	34
β-strand	394-395	2	33
β-strand	413-417	5	30
β-strand	418-419	2	34
β-strand	423-424	2	29
α-helix	426-428	3
β-strand	434-435	2	29
α-helix	436-438	3
β-strand	441-444	4	30
β-strand	447-448	2	30
β-strand	449	1	32
β-strand	451-457	7	33
β-strand	465-470	6	33
α-helix	475-483	9
β-strand	486-491	6	25
β-strand	495-498	4	24

Chain F: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-541	5
α-helix	570-596	27
β-strand	603-609	7	24
α-helix	612-614	3
α-helix	619-620	2
α-helix	621-625	5
α-helix	628-635	8
α-helix	639-663	25

Chain G: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	35
β-strand	10-12	3	36
β-strand	18-25	8	35
α-helix	29-31	3
β-strand	32-39	8	36
β-strand	46-51	6	36
β-strand	58-60	3	36
β-strand	68-73	6	35
α-helix	74-76	3
β-strand	78-83	6	35
α-helix	88-90	3
β-strand	92-101	10	36
β-strand	115	1	36
β-strand	119-123	5	36
β-strand	129	1	37
α-helix	130-131	2
β-strand	132-136	5	38
α-helix	140-144	5
β-strand	149-157	9	38
β-strand	158	1	37
α-helix	161	1
β-strand	162-166	5	39
α-helix	167-169	3
β-strand	176-177	2	38
α-helix	178-180	3
β-strand	181-182	2	38
β-strand	188-195	8	38
β-strand	201	1	40
β-strand	204	1	40
β-strand	206-212	7	39
β-strand	217-223	7	39

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	41
β-strand	10-13	4	42
β-strand	19-24	6	41
β-strand	30	1	43
β-strand	36	1	43
β-strand	38-43	6	42
β-strand	50-54	5	42
β-strand	58-59	2	42
α-helix	60	1
β-strand	67-72	6	41
β-strand	75-80	6	41
α-helix	85-87	3
β-strand	89-95	7	42
α-helix	101	1
β-strand	102-103	2	42
β-strand	107-111	5	42
α-helix	116-118	3
β-strand	119-123	5	44
α-helix	124	1
β-strand	125	1	38
α-helix	126	1
α-helix	127-131	5
β-strand	134-144	11	44
β-strand	149-155	7	45
β-strand	158-159	2	45
β-strand	164-168	5	44
β-strand	178-187	10	44
α-helix	188-192	5
β-strand	196-203	8	45
β-strand	211-215	5	45

4 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
Envelope glycoprotein gp120	A, E, I	protein	463	Human immunodeficiency virus 1	A0A1W6IPB2
Envelope glycoprotein gp41	B, F, J	protein	161	Human immunodeficiency virus 1	Q2N0S7
DH1030.1 Fab Heavy chain	C, G, K	protein	230	Macaca mulatta
DH1030.1 Fab Light Chain	D, H, L	protein	219	Macaca mulatta

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

>8DOW_1 Envelope glycoprotein gp120 (chains A, E, I)
AENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNVWATHACVPTDPSPQELVLGNVT
ENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLICSDATVKTGTVEEMKNCSFN
TTTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINCNTSACTQACPKVTFEPIPIHYC
APAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENLT
NNAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFYATGDIIGDIKQAHCNISEEKWN
DTLQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSFNCGGEFFYCNTSNLFNGTYNGTYI
STNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIAGNITCRSNITGLLLTRDGGTNS
NETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

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

>8DOW_2 Envelope glycoprotein gp41 (chains B, F, J)
VGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQ
HLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIW
DNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>8DOW_3 DH1030.1 Fab Heavy chain (chains C, G, K)
EVQLAESGGGLTKPGGSLRLSCAASGFTFSDFYMDWVRQTPGKGLEWVSRINNDGRNKWY
ADSVRGRFTVSRENAKNTLYLQMDSLRAEDTAVYYCARDRPVYRYWSGGYHLDPWGQGVV
VTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGG

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

>8DOW_4 DH1030.1 Fab Light Chain (chains D, H, L)
YVVMTQSPLSLPITPGQPASISCRSSQRLLHSDGNTYLAWYQQRPGQPPRRLIYEVSKLD
SGVPDRFSGSGAGTDFTLKISRVEAEDVGVYYCGQNTYLPYSFGQGSKVEIKRAVAAPSV
FIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGVLKTGNSQESVTEQDSKDNTYSL
SSTLTLSNTDYQSHNVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Primary citation

Shared recognition mechanism for HIV-1 envelope-reactive V3 glycan broadly neutralizing B cell lineage maturation in humans and macaques. Gobeil, S.M., Janowska, K., Stalls, V. et al. To be published.

Other PDB entries of the same protein (UniProt A0A1W6IPB2), best resolution first:

8SAU 3.3 Å, CryoEM structure of DH270.4-CH848.10.17
8SAW 3.3 Å, CryoEM structure of DH270.UCA.G57R-CH848.10.17DT
8SAY 3.4 Å, CryoEM structure of DH270.3-CH848.10.17
6UM7 3.5 Å, Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex…
8SB2 3.5 Å, CryoEM structure of DH270.I2-CH848.10.17
8DTO 3.57 Å, Vaccine elicited Antibody MU89 bound to CH848.D949.10.17_N133D_N138T.DS.SOSIP.664 HIV-1…
8SB4 3.6 Å, CryoEM structure of DH270.1-CH848.10.17
8VGV 3.6 Å, DH270.6 Fab bound to the HIV-1 CH848 DE3 SOSIP
9AUH 3.6 Å, Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3
8EU8 3.73 Å, Cryo-EM structure of CH848 10.17DT DS-SOSIP-2P Env
9AUG 3.8 Å, Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R
9AUI 3.8 Å, Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA4

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