8DTO: Vaccine elicited Antibody MU89

Vaccine elicited Antibody MU89 bound to CH848.D949.10.17_N133D_N138T.DS.SOSIP.664 HIV-1 Env trimer. Determined by electron microscopy at 3.57 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.57 Å
Organisms: Human immunodeficiency virus 1, Human immunodeficiency virus, Mus musculus
Chains: 12
Atoms: 20,923
Mol. weight: 317.74 kDa
Ligands: NAG
Released: 19 Apr 2023

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

Secondary structure: helices and β-sheets

8DTO contains 66 α-helices and 205 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: 16 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	18
β-strand	36-40	5	19
β-strand	45-47	3	20
β-strand	53-56	4	21
β-strand	67	1	22
α-helix	71-73	3
β-strand	75-76	2	21
α-helix	80-81	2
β-strand	84-85	2	20
β-strand	91-94	4	23
α-helix	95-97	3
α-helix	100-116	17
β-strand	121	1	24
β-strand	129-131	3	25
β-strand	152-160	9	25
β-strand	167-175	9	25
α-helix	176-178	3
β-strand	179-181	3	25
α-helix	182	1
β-strand	190-193	4	25
α-helix	200-201	2
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
α-helix	219-220	2
β-strand	221	1	20
β-strand	223-228	6	20
β-strand	236-239	4	23
β-strand	242-245	4	20
β-strand	247	1	21
β-strand	251	1	26
β-strand	259-261	3	27
α-helix	264-266	3
β-strand	271-273	3	27
β-strand	284-287	4	27
β-strand	294-298	5	28
β-strand	301-302	2	29
β-strand	305-308	4	30
β-strand	316-319	4	30
β-strand	320	1	25
β-strand	322-323	2	29
β-strand	330-334	5	28
α-helix	335-350	16
β-strand	357-361	4	27
α-helix	369-372	4
β-strand	374-375	2	31
β-strand	378	1	32
β-strand	381	1	32
β-strand	382-385	4	31
β-strand	393-395	3	27
β-strand	412-416	5	28
β-strand	417-420	4	31
β-strand	422-423	2	24
α-helix	426-428	3
α-helix	431-432	2
β-strand	433-434	2	24
α-helix	435-437	3
β-strand	442-446	5	28
β-strand	448-455	8	27
β-strand	464-469	6	27
α-helix	475-479	5
β-strand	485-490	6	20
β-strand	493-497	5	19

Chain B: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	531-533	3
α-helix	570-596	27
β-strand	603	1	19
β-strand	609	1	18
α-helix	610-611	2
α-helix	619-625	7
α-helix	628-635	8
α-helix	639-662	24

Chains C and K: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	33
β-strand	10-12	3	34
β-strand	17-25	9	33
β-strand	32-39	8	34
β-strand	45-51	7	34
β-strand	58-60	3	34
β-strand	68-73	6	33
β-strand	78-84	7	33
α-helix	88-90	3
β-strand	92-101	10	34
β-strand	117	1	34
β-strand	121-125	5	34

Chain D: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	35
β-strand	18-23	6	36
α-helix	26-30	5
β-strand	35-40	6	35
β-strand	50	1	35
β-strand	64-69	6	36
β-strand	72-77	6	36
β-strand	87-94	8	35
β-strand	98-101	4	35
β-strand	105-109	5	35

Chain E: 12 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	1
β-strand	36-40	5	2
β-strand	45-47	3	3
β-strand	53-56	4	4
β-strand	67	1	5
α-helix	71-73	3
β-strand	75-76	2	4
α-helix	80-82	3
β-strand	85	1	3
β-strand	91-94	4	6
α-helix	100-116	17
β-strand	121	1	7
β-strand	129-133	5	8
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
β-strand	202-203	2	7
α-helix	204-205	2
β-strand	209	1	5
β-strand	215	1	9
β-strand	216-218	3	4
α-helix	219-220	2
β-strand	221	1	3
β-strand	223-228	6	3
β-strand	236-239	4	6
β-strand	242-245	4	3
β-strand	247	1	4
β-strand	251	1	9
β-strand	259-261	3	10
α-helix	263-266	4
β-strand	271-273	3	10
β-strand	284-298	15	10
β-strand	302	1	11
β-strand	305-308	4	12
β-strand	316-319	4	12
β-strand	320	1	8
β-strand	322	1	11
β-strand	330-334	5	10
α-helix	335-350	16
β-strand	357-361	4	10
β-strand	374-378	5	13
β-strand	381-385	5	13
β-strand	393-395	3	10
β-strand	412-416	5	10
β-strand	417-420	4	13
β-strand	422-424	3	7
α-helix	426-428	3
β-strand	432-434	3	7
α-helix	435-437	3
β-strand	442-456	15	10
β-strand	464-469	6	10
α-helix	475-479	5
β-strand	485-490	6	3
β-strand	493-497	5	2

Chain F: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	570-596	27
β-strand	603	1	2
β-strand	609	1	1
α-helix	610-611	2
α-helix	619-624	6
α-helix	628-634	7
α-helix	639-662	24

Chain G: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
β-strand	10-12	3	15
β-strand	17-25	9	14
β-strand	32-39	8	15
β-strand	45-51	7	15
β-strand	58-60	3	15
β-strand	68-73	6	14
β-strand	78-84	7	14
α-helix	88-90	3
β-strand	92-101	10	15
β-strand	116-117	2	15
β-strand	121-125	5	15

Chains H and L: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	16
β-strand	18-23	6	17
α-helix	26-30	5
β-strand	35-40	6	16
β-strand	50	1	16
β-strand	64-69	6	17
β-strand	72-77	6	17
α-helix	82-84	3
β-strand	87-93	7	16
β-strand	99-101	3	16
β-strand	105-109	5	16

2 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
CH848.3.D0949.10.17chim.6R.DS.SOSIP.664_N133D_N138T gp120	A, E, I	protein	487	Human immunodeficiency virus 1	A0A1W6IPB2
Envelope Glycoprotein gp141	B, F, J	protein	153	Human immunodeficiency virus	Q2N0S6
MU89 Heavy Chain	C, G, K	protein	126	Mus musculus
MU89 Light Chain	D, H, L	protein	106	Mus musculus	A0A5C2G5K7 (AlphaFold model)

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

>8DTO_1 CH848.3.D0949.10.17chim.6R.DS.SOSIP.664_N133D_N138T gp120 (chains A, E, I)
MGSLQPLATLYLLGMLVASVLAAENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNV
WATHACVPTDPSPQELVLGNVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVT
LICSDATVKTGTVEEMKNCSFNTTTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINC
NTSACTQACPKVTFEPIPIHYCAPAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVS
TQLLLNGSLAEKEIVIRSENLTNNAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFY
ATGDIIGDIKQAHCNISEEKWNDTLQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSFNC
GGEFFYCNTSNLFNGTYNGTYISTNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIA
GNITCRSNITGLLLTRDGGTNSNETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTR
CKRRVVG

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

>8DTO_2 Envelope Glycoprotein gp141 (chains B, F, J)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>8DTO_3 MU89 Heavy Chain (chains C, G, K)
QVQLVQSGAEVKKPGASVKVSCKASGYRFTDHYIHWVRQAPGQGPEWMGWINTSSGRSNF
AQKFQGRVTMTRDTSISTAYMELNRLKSDDTAVYYCTTGSWISLYYDSSGYPNFDYWGQG
TLVTVT

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

>8DTO_4 MU89 Light Chain (chains D, H, L)
TQPASVSGSPGQPITISCTGTSSDVGNYDLVSWYQQHPGNAPKYMIYEVTKRPAGISNRF
SGSKSGNTASLTISGLQAEDAADYYCCSYAGSSTVIFGGGTKVTVL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Mutation-guided vaccine design: A process for developing boosting immunogens for HIV broadly neutralizing antibody induction. Wiehe, K., Saunders, K.O., Stalls, V. et al. Cell Host Microbe (2024) 32:693-709.e7. DOI 10.1016/j.chom.2024.04.006 · 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
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
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

Browse structure collections

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