8VGV: DH270.6 Fab

DH270.6 Fab bound to the HIV-1 CH848 DE3 SOSIP. Determined by electron microscopy at 3.6 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 19,632
Mol. weight: 287.91 kDa
Released: 2 Oct 2024

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

Secondary structure: helices and β-sheets

8VGV contains 87 α-helices and 194 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: 15 helices, 43 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	55-56	2	4
α-helix	64-67	4
β-strand	68	1	5
β-strand	75-76	2	4
β-strand	85	1	2
β-strand	91-94	4	6
α-helix	100-116	17
β-strand	121	1	7
α-helix	123-125	3
β-strand	129-133	5	8
α-helix	136-138	3
β-strand	152-160	9	8
β-strand	167-175	9	8
β-strand	179-181	3	8
α-helix	182	1
β-strand	190-193	4	8
α-helix	194-197	4
α-helix	201	1
β-strand	202-203	2	7
α-helix	204	1
β-strand	209	1	5
β-strand	215	1	9
β-strand	218	1	3
β-strand	223-228	6	2
β-strand	236-239	4	6
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	9
β-strand	261	1	10
β-strand	271-273	3	10
β-strand	284-298	15	10
β-strand	302	1	11
β-strand	305-309	5	12
β-strand	315-319	5	12
β-strand	322	1	11
β-strand	330-334	5	10
α-helix	335-352	18
β-strand	357-361	4	10
α-helix	369-372	4
β-strand	374-375	2	13
α-helix	378-380	3
β-strand	382-385	4	13
β-strand	393-395	3	10
β-strand	413-417	5	10
β-strand	418-421	4	13
β-strand	423-424	2	7
α-helix	426-428	3
α-helix	430-432	3
β-strand	434-435	2	7
α-helix	436-438	3
β-strand	443-457	15	10
β-strand	465-470	6	10
α-helix	476-480	5
β-strand	486-491	6	2
β-strand	494-498	5	1

Chain B: 10 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	515-518	4
α-helix	529-533	5
α-helix	537-541	5
α-helix	570-572	3
α-helix	573-596	24
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	612-614	3
α-helix	619-625	7
α-helix	628-635	8
α-helix	639-663	25

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	32-39	8	15
β-strand	45-51	7	15
β-strand	58-60	3	15
α-helix	62-64	3
β-strand	65	1	14
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-101	10	15
β-strand	117	1	15
β-strand	121-125	5	15

Chain D: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	16
β-strand	9-12	4	17
β-strand	18-23	6	16
β-strand	35-40	6	17
β-strand	47-50	4	17
β-strand	64-69	6	16
β-strand	72-77	6	16
α-helix	82-84	3
β-strand	87-93	7	17
β-strand	99-101	3	17
β-strand	105-109	5	17

Chain E: 12 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	18
β-strand	45-47	3	19
β-strand	53	1	20
β-strand	55-56	2	21
α-helix	64-67	4
β-strand	68	1	22
β-strand	75-76	2	21
β-strand	84-85	2	19
β-strand	91-94	4	23
α-helix	100-116	17
β-strand	121	1	24
α-helix	123-125	3
β-strand	129-130	2	25
β-strand	133-136	4	25
β-strand	139-160	14	25
β-strand	167-175	9	25
β-strand	179-181	3	25
β-strand	190-193	4	25
α-helix	194-197	4
α-helix	201	1
β-strand	202-203	2	24
α-helix	204	1
β-strand	209	1	22
β-strand	215	1	21
β-strand	218	1	20
β-strand	223-228	6	19
β-strand	236-239	4	23
β-strand	242-245	4	19
β-strand	247	1	20
β-strand	251	1	21
β-strand	259-261	3	26
β-strand	271-273	3	26
β-strand	284-298	15	26
β-strand	302-309	8	27
β-strand	315-322	9	27
β-strand	330-334	5	26
α-helix	335-352	18
β-strand	357-361	4	26
α-helix	369-372	4
β-strand	374-375	2	28
α-helix	378-380	3
β-strand	382-385	4	28
β-strand	394-395	2	26
β-strand	413-417	5	26
β-strand	418-421	4	28
β-strand	423-424	2	24
α-helix	426-428	3
β-strand	434-435	2	24
α-helix	436-438	3
β-strand	443-457	15	26
β-strand	465-470	6	26
α-helix	476-480	5
β-strand	486-491	6	19
β-strand	495-498	4	18

Chain F: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	515-519	5
α-helix	529-533	5
α-helix	537-541	5
α-helix	542-544	3
α-helix	570-572	3
α-helix	573-596	24
β-strand	603-609	7	18
α-helix	610-611	2
α-helix	612-614	3
α-helix	619-625	7
α-helix	628-635	8
α-helix	639-663	25

Chains G and K: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	29
β-strand	10-12	3	30
β-strand	18-25	8	29
α-helix	29-31	3
β-strand	32-39	8	30
β-strand	45-51	7	30
β-strand	58-60	3	30
α-helix	62-64	3
β-strand	68-73	6	29
β-strand	78-83	6	29
α-helix	88-90	3
β-strand	92-101	10	30
β-strand	117	1	30
β-strand	121-125	5	30

Chain H: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	31
β-strand	9-12	4	32
β-strand	18-23	6	31
α-helix	26-30	5
β-strand	35-40	6	32
β-strand	47-50	4	32
β-strand	64-69	6	31
β-strand	72-77	6	31
α-helix	82-84	3
β-strand	87-94	8	32
β-strand	98-101	4	32
β-strand	105-109	5	32

3 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
CH848 DE3 SOSIP gp120	A, E, I	protein	462	Human immunodeficiency virus 1	A0A1W6IPB2
CH848 DE3 SOSIP gp41	B, F, J	protein	153	Human immunodeficiency virus 1	A0A1W6IPB2
DH270.6 Antibody Fab Heavy Chain	C, G, K	protein	126	Homo sapiens
DH270.6 Antibody Fab Light Chain	D, H, L	protein	108	Homo sapiens

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

>8VGV_1 CH848 DE3 SOSIP gp120 (chains A, E, I)
ENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNVWATHACVPTDPSPQELVLGNVTE
NFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLICSDATVKTGTVEEMKNCSFNT
TTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINCNTSACTQACPKVTFEPIPIHYCA
PAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENLTN
NAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFYATGDIIGDIKQAHCNISEEKWND
TLQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSFNCGGEFFYCNTSNLFNGTYNGTYIS
TNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIAGNITCRSNITGLLLTRDGGTNSN
ETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

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

>8VGV_2 CH848 DE3 SOSIP gp41 (chains B, F, J)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>8VGV_3 DH270.6 Antibody Fab Heavy Chain (chains C, G, K)
QVQLVQSGAQMKNPGASVKVSCAPSGYTFTDFYIHWLRQAPGQGLQWMGWMNPQTGRTNT
ARNFQGRVTMTRDTSIGTAYMELRSLTSDDTAIYYCTTGGWISLYYDSSYYPNFDHWGQG
TLLTVS

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

>8VGV_4 DH270.6 Antibody Fab Light Chain (chains D, H, L)
ALTQPASVSGSPGQSITISCTGTKYDVGSHDLVSWYQQYPGKVPKYMIYEVNKRPSGVSN
RFSGSKSGNTASLTISGLRAEDEADYYCCSFGGSATVVCGGGTKVTVL

Primary citation

Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies. Henderson, R., Anasti, K., Manne, K. et al. Nat Commun (2024) 15:9503-9503. DOI 10.1038/s41467-024-53120-9 · PubMed

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
9AUH 3.6 Å, Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3
8DOW 3.69 Å, Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
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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