8SB2: DH270.I2-CH848.10.17

CryoEM structure of DH270.I2-CH848.10.17. Determined by electron microscopy at 3.5 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: HIV-1 06TG.HT008, Homo sapiens
Chains: 12
Atoms: 20,186
Mol. weight: 294.17 kDa
Released: 19 Apr 2023

Explore 8SB2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SB2 contains 68 α-helices and 180 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: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53-56	4	3
α-helix	58-62	5
α-helix	69-73	5
α-helix	74	1
β-strand	75-76	2	3
α-helix	77	1
β-strand	84-85	2	2
β-strand	91-94	4	4
α-helix	100-114	15
α-helix	128	1
β-strand	129-135	7	5
β-strand	150-162	13	5
β-strand	169-177	9	5
α-helix	178-180	3
β-strand	181-183	3	5
β-strand	190-193	4	5
α-helix	201	1
β-strand	202-203	2	6
α-helix	204-205	2
β-strand	215	1	7
β-strand	216-218	3	3
α-helix	219-220	2
β-strand	223-228	6	2
β-strand	236-239	4	4
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	7
β-strand	259-261	3	8
β-strand	271-273	3	8
β-strand	284-298	15	8
β-strand	302-308	7	5
β-strand	316-322	8	5
β-strand	330-334	5	8
α-helix	335-350	16
β-strand	359-361	3	8
α-helix	369-372	4
β-strand	374-378	5	9
β-strand	381-385	5	9
β-strand	393-395	3	8
β-strand	413-417	5	8
β-strand	418-421	4	9
β-strand	423-425	3	6
β-strand	433-435	3	6
α-helix	436-438	3
β-strand	443-456	14	8
β-strand	468-470	3	8
α-helix	476-480	5
β-strand	486-491	6	2
β-strand	494-499	6	1

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	537-542	6
α-helix	572-595	24
β-strand	603-609	7	1
α-helix	612-614	3
α-helix	620-623	4
α-helix	628-635	8
α-helix	639-643	5
α-helix	650-662	13

Chains C and M: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	10
β-strand	10-12	3	11
β-strand	18-25	8	10
β-strand	32-39	8	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-83	6	10
β-strand	92-101	10	11
β-strand	117	1	11
β-strand	121-125	5	11

Chains D, I and N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	12
β-strand	9-12	4	13
β-strand	17-23	7	12
β-strand	35-40	6	13
β-strand	47-51	5	13
β-strand	55	1	13
β-strand	64-69	6	12
β-strand	72-78	7	12
α-helix	82-84	3
β-strand	86-93	8	13
β-strand	99-101	3	13
β-strand	105-109	5	13

Chain F: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	14
β-strand	45-47	3	15
β-strand	53-56	4	16
α-helix	58-62	5
α-helix	69-73	5
α-helix	74	1
β-strand	75-76	2	16
α-helix	77	1
β-strand	84-85	2	15
β-strand	91-94	4	17
α-helix	100-115	16
α-helix	128	1
β-strand	129-135	7	18
β-strand	150-162	13	18
β-strand	169-177	9	18
α-helix	178-180	3
β-strand	181-183	3	18
β-strand	190-193	4	18
α-helix	201	1
β-strand	202-203	2	19
α-helix	204-205	2
β-strand	215	1	20
β-strand	216-218	3	16
β-strand	223-228	6	15
β-strand	236-239	4	17
β-strand	242-245	4	15
β-strand	247	1	16
β-strand	251	1	20
β-strand	259-261	3	21
β-strand	271-273	3	21
β-strand	284-298	15	21
β-strand	302-308	7	18
β-strand	316-322	8	18
β-strand	330-334	5	21
α-helix	335-350	16
β-strand	359-361	3	21
α-helix	369-372	4
β-strand	374-378	5	22
β-strand	381-385	5	22
β-strand	393-395	3	21
β-strand	413-417	5	21
β-strand	418-421	4	22
β-strand	423-424	2	19
β-strand	434-435	2	19
α-helix	436-438	3
β-strand	443-456	14	21
α-helix	457-458	2
β-strand	468-470	3	21
α-helix	476-480	5
β-strand	486-491	6	15
β-strand	494-499	6	14

Chain G: 10 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	537-542	6
α-helix	572-595	24
β-strand	603-609	7	14
α-helix	610-611	2
α-helix	612-614	3
α-helix	620-623	4
α-helix	628-635	8
α-helix	639-645	7
α-helix	651-653	3
α-helix	656-658	3
α-helix	659-663	5

Chain H: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	23
β-strand	10-12	3	24
β-strand	18-23	6	23
β-strand	32-39	8	24
β-strand	45-51	7	24
β-strand	58-60	3	24
β-strand	68-73	6	23
β-strand	78-83	6	23
β-strand	92-101	10	24
β-strand	117	1	24
β-strand	121-125	5	24

Chain K: 13 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	27
β-strand	45-47	3	28
β-strand	53-56	4	29
α-helix	58-62	5
α-helix	69-73	5
α-helix	74	1
β-strand	75-76	2	29
α-helix	77	1
β-strand	84-85	2	28
β-strand	91-94	4	30
α-helix	100-114	15
α-helix	128	1
β-strand	129-135	7	31
β-strand	150-162	13	31
β-strand	169-177	9	31
α-helix	178-180	3
β-strand	181-183	3	31
β-strand	190-193	4	31
α-helix	201	1
β-strand	202-203	2	32
α-helix	204-205	2
β-strand	215	1	33
β-strand	216-218	3	29
β-strand	223-228	6	28
β-strand	236-239	4	30
β-strand	242-245	4	28
β-strand	247	1	29
β-strand	251	1	33
β-strand	259-261	3	34
β-strand	271-273	3	34
β-strand	284-298	15	34
β-strand	304-308	5	31
β-strand	316-320	5	31
β-strand	330-334	5	34
α-helix	335-350	16
β-strand	359-361	3	34
α-helix	369-372	4
β-strand	374-377	4	35
β-strand	382-385	4	35
β-strand	393-395	3	34
β-strand	413-417	5	34
β-strand	418-421	4	35
β-strand	423-425	3	32
β-strand	433-435	3	32
α-helix	436-438	3
β-strand	443-456	14	34
β-strand	468-470	3	34
α-helix	476-480	5
β-strand	486-491	6	28
β-strand	494-499	6	27

1 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
CH848.10.17.SOSIP gp120	A, F, K	protein	471	HIV-1 06TG.HT008	A0A1W6IPB2
CH848.10.17.SOSIP gp41	B, G, L	protein	132	HIV-1 06TG.HT008	Q9IWR0
DH270.I2.6 variable heavy chain	C, H, M	protein	127	Homo sapiens
DH270.I2.6 variable light chain	D, I, N	protein	110	Homo sapiens	A0A5C2G1R5 (AlphaFold model), A0A5C2G5B3 (AlphaFold model)

Sequence of entity 1 (A, F, K), FASTA

>8SB2_1 CH848.10.17.SOSIP gp120 (chains A, F, K)
AENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNVWATHACVPTDPSPQELVLGNVT
ENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLICSNATVKNGTVEEMKNCSFN
TTTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINCNTSACTQACPKVTFEPIPIHYC
APAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENLT
NNAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFYATGDIIGDIKQAHCNISEEKWN
DTLQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSFNCGGEFFYCNTSNLFNGTYNGTYI
STNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIAGNITCRSNITGLLLTRDGGTNS
NETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Sequence of entity 2 (B, G, L), FASTA

>8SB2_2 CH848.10.17.SOSIP gp41 (chains B, G, L)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGTVWGIKQLQARVLAVERYLRDQQL
LGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQ
QEKNEQDLLALD

Sequence of entity 3 (C, H, M), FASTA

>8SB2_3 DH270.I2.6 variable heavy chain (chains C, H, M)
QVQLVQSGAEMKNPGASVKVSCAASGYTFTDFYIHWVRQAPGQGLQWMGWMNPKTGRTNT
AQNFQGRVTMTRDTSIGTAYMELRSLTSDDTAVYYCATGGWISLYYDSSYYPNFDHWGQG
TLVTVSS

Sequence of entity 4 (D, I, N), FASTA

>8SB2_4 DH270.I2.6 variable light chain (chains D, I, N)
QSALTQPASVSGSPGQSITISCTGTSYDVGSYDLVSWYQQHPGKAPKYMIYEVNKRPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCCSFGGSATVVCGGGTKVTVL

Primary citation

Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage. Henderson, R., Zhou, Y., Stalls, V. et al. Nat Commun (2023) 14:2782-2782. DOI 10.1038/s41467-023-38108-1 · 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…
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
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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