8SAU: DH270.4-CH848.10.17

CryoEM structure of DH270.4-CH848.10.17. Determined by electron microscopy at 3.3 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: HIV-1 06TG.HT008, Homo sapiens
Chains: 12
Atoms: 19,884
Mol. weight: 286.62 kDa
Released: 19 Apr 2023

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

Secondary structure: helices and β-sheets

8SAU contains 77 α-helices and 203 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, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
α-helix	52	1
β-strand	53-56	4	3
α-helix	58-60	3
α-helix	69-72	4
β-strand	75-76	2	3
α-helix	80	1
α-helix	82-83	2
β-strand	84-86	3	2
β-strand	91-94	4	4
α-helix	100-115	16
α-helix	123-125	3
β-strand	129-131	3	5
β-strand	155-162	8	5
β-strand	169-176	8	5
α-helix	178-180	3
β-strand	181-183	3	5
β-strand	190-193	4	5
β-strand	203	1	6
α-helix	204-205	2
β-strand	215	1	7
β-strand	216-218	3	3
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	256	1	8
β-strand	259-260	2	9
β-strand	271-273	3	9
α-helix	283	1
β-strand	284-300	17	9
β-strand	301	1	10
β-strand	302	1	9
β-strand	304-308	5	5
β-strand	316-320	5	5
α-helix	321c-322	2
β-strand	323	1	10
β-strand	330-334	5	9
α-helix	335-349	15
α-helix	369-372	4
β-strand	374-377	4	8
β-strand	382-385	4	8
β-strand	396	1	11
β-strand	398	1	11
β-strand	413-417	5	9
β-strand	418-421	4	8
β-strand	423-425	3	6
β-strand	433-435	3	6
α-helix	436-440	5
β-strand	441-456	16	9
α-helix	457-459	3
β-strand	468-470	3	9
α-helix	475-480	6
α-helix	483-485	3
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	530-533	4
α-helix	538-541	4
α-helix	572-595	24
β-strand	603-609	7	1
α-helix	612-614	3
α-helix	619-623	5
α-helix	628-635	8
α-helix	639-663	25

Chains C and H: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	12
β-strand	6	1	13
β-strand	18-22	5	13
β-strand	25-26	2	12
β-strand	32-39	8	14
β-strand	45-51	7	14
β-strand	58-60	3	14
α-helix	62-64	3
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-94	3	15
β-strand	95-101	7	14
β-strand	116-117	2	14
β-strand	121-123	3	15

Chain D: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	16
β-strand	5	1	17
β-strand	10-12	3	18
β-strand	19-23	5	17
β-strand	35-40	6	19
α-helix	41	1
β-strand	46-50	5	19
β-strand	51	1	20
β-strand	55	1	20
β-strand	65	1	17
β-strand	69	1	17
β-strand	72-76	5	17
β-strand	89-94	6	19
β-strand	98-101	4	19
β-strand	102	1	16
β-strand	107-109	3	18

Chain F: 12 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	21
β-strand	45-46	2	22
α-helix	51-52	2
β-strand	53-56	4	23
α-helix	58-60	3
α-helix	69-72	4
β-strand	75-76	2	23
β-strand	84-86	3	22
β-strand	91-94	4	24
α-helix	100-115	16
α-helix	123-125	3
β-strand	129-131	3	25
β-strand	155-158	4	25
β-strand	161-162	2	26
β-strand	169-170	2	26
β-strand	173-176	4	25
α-helix	178-180	3
β-strand	181-183	3	25
β-strand	190-193	4	25
β-strand	203	1	27
α-helix	204-205	2
β-strand	215	1	28
β-strand	216-218	3	23
β-strand	223-228	6	22
β-strand	236-239	4	24
β-strand	242-245	4	22
β-strand	247	1	23
β-strand	251	1	28
β-strand	256	1	29
β-strand	259-261	3	30
β-strand	271-273	3	30
α-helix	283	1
β-strand	284-300	17	30
β-strand	301-308	8	25
β-strand	316-323	9	25
β-strand	330-334	5	30
α-helix	335-349	15
α-helix	369-372	4
β-strand	374-377	4	29
β-strand	382-385	4	29
β-strand	413-417	5	30
β-strand	418-421	4	29
β-strand	423-425	3	27
β-strand	433-435	3	27
β-strand	441-456	16	30
α-helix	457-459	3
β-strand	468-470	3	30
α-helix	475-480	6
β-strand	486-491	6	22
β-strand	494-499	6	21

Chain G: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	538-541	4
α-helix	542-544	3
α-helix	573-595	23
β-strand	603-609	7	21
α-helix	612-614	3
α-helix	619-623	5
α-helix	628-635	8
α-helix	639-663	25

Chain I: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	35
β-strand	5	1	36
β-strand	10-12	3	37
β-strand	19-23	5	36
β-strand	35-40	6	38
α-helix	41	1
β-strand	46-50	5	38
β-strand	51	1	39
β-strand	55	1	39
β-strand	65-69	5	36
β-strand	72-76	5	36
β-strand	89-94	6	38
β-strand	98-101	4	38
β-strand	102	1	35
β-strand	107-109	3	37

Chain K: 16 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	40
β-strand	45-46	2	41
α-helix	52	1
β-strand	53-56	4	42
α-helix	58-60	3
α-helix	69-72	4
β-strand	75-76	2	42
α-helix	80	1
α-helix	82-83	2
β-strand	84-86	3	41
β-strand	91-94	4	43
α-helix	100-115	16
α-helix	123-125	3
β-strand	129-132	4	44
β-strand	155-162	8	44
β-strand	169-176	8	44
α-helix	178-180	3
β-strand	181-183	3	44
β-strand	190-193	4	44
β-strand	203	1	45
α-helix	204-205	2
β-strand	215	1	46
β-strand	216-218	3	42
β-strand	223-228	6	41
β-strand	236-239	4	43
β-strand	242-245	4	41
β-strand	251	1	46
β-strand	256	1	47
β-strand	259-260	2	48
β-strand	271-273	3	48
β-strand	284-300	17	48
β-strand	301	1	49
β-strand	302	1	48
β-strand	304-308	5	44
β-strand	316-320	5	44
α-helix	321c-322	2
β-strand	323	1	49
β-strand	330-334	5	48
α-helix	335-349	15
β-strand	360-361	2	48
α-helix	369-372	4
β-strand	374-377	4	47
β-strand	382-385	4	47
β-strand	413-417	5	48
β-strand	418-421	4	47
β-strand	423-425	3	45
β-strand	433-435	3	45
α-helix	436-438	3
β-strand	441-456	16	48
α-helix	457-459	3
β-strand	467-470	4	48
α-helix	475-480	6
α-helix	483-485	3
β-strand	486-491	6	41
β-strand	494-499	6	40

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
CH848.10.17 gp120	A, F, K	protein	463	HIV-1 06TG.HT008	A0A1W6IPB2
CH848.10.17 gp41	B, G, L	protein	132	HIV-1 06TG.HT008
DH270.4 variable heavy chain	C, H, M	protein	126	Homo sapiens
DH270.4 variable light chain	D, I, N	protein	110	Homo sapiens

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

>8SAU_1 CH848.10.17 gp120 (chains A, F, K)
AENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNVWATHACVPTDPSPQELVLGNVT
ENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLICSNATVKNGTVEEMKNCSFN
TTTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINCNTSACTQACPKVTFEPIPIHYC
APAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENLT
NNAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFYATGDIIGDIKQAHCNISEEKWN
DTLQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSFNCGGEFFYCNTSNLFNGTYNGTYI
STNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIAGNITCRSNITGLLLTRDGGTNS
NETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

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

>8SAU_2 CH848.10.17 gp41 (chains B, G, L)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGTVWGIKQLQARVLAVERYLRDQQL
LGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQ
QEKNEQDLLALD

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

>8SAU_3 DH270.4 variable heavy chain (chains C, H, M)
EVQLVQSGAEMKNPGASVKVSCAASGYGFTDFYIHWVRLAPGHGLQWMGWMNPKTGRTNN
AQDFQGRVTLTRDTSIGTAYMELRRLTSDDTAVYYCVTGGWISPYYDSSYYPNFDHWGQG
TLITVS

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

>8SAU_4 DH270.4 variable light chain (chains D, I, N)
QSALTQPASVSGSPGQSITISCTGTSYDVAKFDLVSWFQQHPGKAPKYMIYEVNKWPSGV
SHRFSGSKSGNTASLTISGLQAEDEADYYCCSFGGSATVVCGGGTKVTVL

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:

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
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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