8SB4: DH270.1-CH848.10.17

CryoEM structure of DH270.1-CH848.10.17. Determined by electron microscopy at 3.6 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: HIV-1 06TG.HT008, Homo sapiens
Chains: 12
Atoms: 20,041
Mol. weight: 286.7 kDa
Released: 19 Apr 2023

Explore 8SB4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SB4 contains 77 α-helices and 190 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: 10 helices, 35 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	70-73	4
β-strand	75-76	2	3
β-strand	84-85	2	2
β-strand	91-94	4	4
α-helix	99-115	17
β-strand	129-132	4	5
β-strand	155-163	9	5
β-strand	166-176	11	5
α-helix	178-180	3
β-strand	181-183	3	5
β-strand	190-193	4	5
β-strand	202-203	2	6
α-helix	204-205	2
β-strand	215-218	4	3
β-strand	223-228	6	2
β-strand	236-239	4	4
β-strand	242-245	4	2
β-strand	247	1	3
α-helix	248-250	3
β-strand	251	1	3
β-strand	259	1	5
β-strand	271-273	3	5
β-strand	284-308	25	5
β-strand	316-323	9	5
β-strand	330-333	4	5
α-helix	335-350	16
β-strand	359-361	3	5
α-helix	369-372	4
β-strand	374-379	6	5
β-strand	381-386	6	5
β-strand	393-395	3	5
β-strand	414-421	8	5
β-strand	423-425	3	6
β-strand	433-435	3	6
α-helix	436-438	3
β-strand	441-444	4	5
β-strand	447-456	10	5
α-helix	457-459	3
β-strand	467-470	4	5
α-helix	476-480	5
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains B and G: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-534	5
α-helix	538-541	4
α-helix	574-595	22
β-strand	603-609	7	1
α-helix	610	1
α-helix	612-614	3
α-helix	619-623	5
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-663	25

Chain C: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	32-39	8	8
α-helix	44-45	2
β-strand	46-51	6	8
β-strand	58-59	2	8
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-101	10	8
α-helix	102	1
β-strand	103	1	9
β-strand	106	1	9
β-strand	116-117	2	8
β-strand	121-123	3	8

Chain D: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	10
β-strand	5	1	11
β-strand	9	1	12
β-strand	12	1	13
β-strand	20-23	4	11
α-helix	26-30	5
β-strand	35-40	6	14
β-strand	47-50	4	14
β-strand	51	1	15
β-strand	55	1	15
β-strand	65-69	5	11
β-strand	72-76	5	11
α-helix	82-84	3
β-strand	87-93	7	14
β-strand	99-101	3	14
β-strand	102	1	10
β-strand	106	1	12
β-strand	109	1	13

Chain F: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	16
β-strand	45-47	3	17
β-strand	53-56	4	18
α-helix	58-60	3
α-helix	69-71	3
β-strand	75-76	2	18
β-strand	84-85	2	17
β-strand	91-94	4	19
α-helix	99-115	17
β-strand	129-132	4	20
β-strand	155-161	7	20
β-strand	170-176	7	20
α-helix	178-180	3
β-strand	181-183	3	20
β-strand	190-193	4	20
β-strand	202-203	2	21
α-helix	204-205	2
β-strand	215-218	4	18
β-strand	223-228	6	17
β-strand	236-239	4	19
β-strand	242-245	4	17
β-strand	247	1	18
α-helix	248-250	3
β-strand	251	1	18
β-strand	259-260	2	20
α-helix	264-266	3
β-strand	271-273	3	20
β-strand	284-308	25	20
β-strand	316-323	9	20
β-strand	330-333	4	20
α-helix	335-350	16
β-strand	359-361	3	20
α-helix	369-372	4
β-strand	374-379	6	20
β-strand	381-386	6	20
β-strand	394-395	2	20
β-strand	414-421	8	20
β-strand	423-425	3	21
β-strand	433-435	3	21
α-helix	436-438	3
β-strand	441-444	4	20
β-strand	447-456	10	20
α-helix	457-459	3
β-strand	467-470	4	20
α-helix	476-480	5
β-strand	486-491	6	17
β-strand	494-499	6	16

Chain H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
β-strand	18-25	8	22
α-helix	29-31	3
β-strand	32-39	8	23
α-helix	44-45	2
β-strand	46-51	6	23
β-strand	58-59	2	23
β-strand	68-73	6	22
β-strand	78-83	6	22
α-helix	88-90	3
β-strand	92-101	10	23
β-strand	103	1	24
β-strand	106	1	24
β-strand	117	1	23
β-strand	121-123	3	23

Chain I: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	25
β-strand	5	1	26
β-strand	9-12	4	27
β-strand	20-22	3	28
β-strand	23	1	26
α-helix	26-30	5
β-strand	35-40	6	29
β-strand	47-50	4	29
β-strand	51	1	30
β-strand	55	1	30
β-strand	65-69	5	28
β-strand	72-76	5	28
α-helix	82-84	3
β-strand	87-93	7	29
β-strand	99-101	3	29
β-strand	102	1	25
β-strand	106-109	4	27

Chain K: 12 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	31
β-strand	45-47	3	32
β-strand	53-56	4	33
α-helix	58-60	3
α-helix	70-73	4
β-strand	75-76	2	33
β-strand	84-86	3	32
β-strand	91-94	4	34
α-helix	99-115	17
β-strand	129-132	4	35
β-strand	155-163	9	35
β-strand	166-176	11	35
α-helix	178-180	3
β-strand	181-183	3	35
β-strand	190-193	4	35
β-strand	202-203	2	36
α-helix	204-205	2
β-strand	215-218	4	33
β-strand	223-228	6	32
β-strand	236-239	4	34
β-strand	242-245	4	32
β-strand	247	1	33
α-helix	248-250	3
β-strand	251	1	33
β-strand	256	1	35
β-strand	259	1	35
β-strand	271-273	3	35
β-strand	284-308	25	35
β-strand	316-323	9	35
β-strand	330-334	5	35
α-helix	335-350	16
β-strand	359-361	3	35
α-helix	369-372	4
β-strand	374-379	6	35
β-strand	381-386	6	35
β-strand	394-395	2	35
β-strand	413-421	9	35
β-strand	423-425	3	36
β-strand	433-435	3	36
α-helix	436-438	3
β-strand	441-444	4	35
β-strand	447-456	10	35
α-helix	457-459	3
β-strand	467-470	4	35
α-helix	476-480	5
α-helix	483-485	3
β-strand	486-491	6	32
β-strand	494-499	6	31

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
DH270.1 variable heavy chain	C, H, M	protein	126	Homo sapiens
DH270.1 variable light chain	D, I, N	protein	110	Homo sapiens

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

>8SB4_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

>8SB4_2 CH848.10.17 gp41 (chains B, G, L)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGTVWGIKQLQARVLAVERYLRDQQL
LGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQ
QEKNEQDLLALD

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

>8SB4_3 DH270.1 variable heavy chain (chains C, H, M)
QVQLVQSGAEMKKPGASVRVSCKASGYTFTDYYIHWVRQAPGQGPEWMGWINPSTGRTNS
PQKFQGRVTMTRDTSISTAYMDLNRLTSDDTAMYYCTTGGWIGLYSDTSGYPNFDYWGQG
TLVTVS

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

>8SB4_4 DH270.1 variable light chain (chains D, I, N)
QSALTQPASVSGSPGQSITISCTGTNYDVGSYNLVSWYQQHPGKVPKYIIYEVNKRPSGV
SNRFSGSKSGNTASLTISGLQAEDEATYYCCSYAGSSIIFFGGGTKLTVI

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…
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…
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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