8SAY: DH270.3-CH848.10.17

CryoEM structure of DH270.3-CH848.10.17. Determined by electron microscopy at 3.4 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: HIV-1 06TG.HT008, Homo sapiens
Chains: 12
Atoms: 19,902
Mol. weight: 287.68 kDa
Released: 19 Apr 2023

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

Secondary structure: helices and β-sheets

8SAY contains 92 α-helices and 230 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, 48 β-strands

Element	Residues	Length	Sheet
α-helix	34	1
β-strand	35	1	1
β-strand	36	1	2
β-strand	38	1	3
β-strand	39-40	2	4
β-strand	45-46	2	5
β-strand	53-56	4	6
α-helix	58-62	5
α-helix	70-73	4
β-strand	75-76	2	6
β-strand	84-85	2	5
β-strand	91-92	2	7
α-helix	100-115	16
β-strand	128-131	4	8
β-strand	155-162	8	8
β-strand	169-176	8	8
α-helix	178-180	3
β-strand	181-183	3	8
β-strand	190-193	4	8
β-strand	203	1	9
α-helix	204-205	2
β-strand	215-218	4	6
α-helix	219-220	2
β-strand	223-228	6	5
β-strand	238-239	2	7
β-strand	242-245	4	5
β-strand	247	1	6
α-helix	248-250	3
β-strand	251	1	6
β-strand	256	1	10
β-strand	259	1	11
β-strand	272-273	2	11
β-strand	283-294	12	11
β-strand	295-297	3	12
β-strand	301	1	13
β-strand	302	1	14
β-strand	304-308	5	8
β-strand	316-320	5	8
α-helix	321C-322	2
β-strand	323	1	13
β-strand	330-332	3	12
β-strand	333	1	15
α-helix	335-349	15
β-strand	359-361	3	11
β-strand	374-378	5	10
β-strand	381-385	5	10
β-strand	393-395	3	11
α-helix	403	1
α-helix	405	1
β-strand	414	1	15
β-strand	418-420	3	10
β-strand	423-425	3	9
β-strand	433-435	3	9
β-strand	441	1	14
β-strand	444	1	12
β-strand	447-456	10	11
α-helix	457-459	3
β-strand	468-470	3	11
α-helix	475-480	6
β-strand	486-491	6	5
β-strand	494-495	2	4
β-strand	498	1	2

Chain B: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	529	1	16
α-helix	530-534	5
α-helix	538-542	5
α-helix	572-578	7
α-helix	581	1
α-helix	582-586	5
α-helix	587-595	9
β-strand	604	1	3
α-helix	608	1
β-strand	609	1	1
α-helix	610	1
α-helix	612-615	4
α-helix	619-625	7
β-strand	627	1	16
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-660	22

Chain C: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	17
β-strand	6	1	18
α-helix	7-9	3
β-strand	10-11	2	19
β-strand	17-23	7	18
β-strand	25	1	17
α-helix	29-31	3
β-strand	32-39	8	20
β-strand	45-52	8	20
β-strand	57-59	3	20
β-strand	65	1	18
β-strand	68-73	6	18
β-strand	78-84	7	18
α-helix	88-90	3
β-strand	92-94	3	19
β-strand	95-101	7	20
β-strand	103	1	21
β-strand	106	1	21
β-strand	117	1	20
β-strand	121-124	4	19

Chain D: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	235	1	22
β-strand	240-241	2	23
β-strand	247-248	2	24
β-strand	251-253	3	22
α-helix	256-260	5
β-strand	265-270	6	25
β-strand	276-281	6	25
β-strand	285-286	2	25
β-strand	297-299	3	22
β-strand	302-304	3	22
β-strand	307-308	2	24
β-strand	317-324	8	25
β-strand	328-331	4	25
β-strand	336	1	25
β-strand	337-338	2	23

Chain F: 14 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	34	1
β-strand	35	1	26
β-strand	36	1	27
β-strand	38	1	28
β-strand	39-40	2	29
β-strand	45-46	2	30
β-strand	53-56	4	31
α-helix	58-62	5
α-helix	69-71	3
β-strand	75-76	2	31
β-strand	84-85	2	30
β-strand	91-94	4	32
α-helix	100-115	16
β-strand	128-131	4	33
β-strand	155-162	8	33
β-strand	169-176	8	33
α-helix	178-180	3
β-strand	181-183	3	33
β-strand	190-193	4	33
β-strand	202-203	2	34
α-helix	204-205	2
β-strand	215-218	4	31
α-helix	219-220	2
β-strand	223-228	6	30
β-strand	236-239	4	32
β-strand	242-245	4	30
β-strand	247	1	31
α-helix	248-250	3
β-strand	251	1	31
β-strand	256	1	35
β-strand	259-260	2	36
β-strand	272-273	2	36
β-strand	283-294	12	36
β-strand	295-297	3	35
β-strand	301	1	37
β-strand	302	1	38
β-strand	304-308	5	33
β-strand	316-320	5	33
α-helix	321C-322	2
β-strand	323	1	37
β-strand	329-333	5	35
α-helix	335-349	15
β-strand	359-361	3	36
β-strand	374-378	5	35
β-strand	381-386	6	35
β-strand	393-395	3	36
α-helix	403	1
α-helix	405	1
β-strand	414-420	7	35
β-strand	423-425	3	34
β-strand	433-435	3	34
α-helix	437-439	3
β-strand	441	1	38
β-strand	444	1	35
β-strand	447-456	10	36
β-strand	468-470	3	36
α-helix	475-480	6
β-strand	486-491	6	30
β-strand	494-495	2	29
β-strand	498	1	27

Chain G: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	530-534	5
α-helix	538-541	4
α-helix	572-578	7
α-helix	581-595	15
β-strand	604	1	28
β-strand	609	1	26
α-helix	612-615	4
α-helix	619-625	7
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-661	23

Chain H: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	39
α-helix	5	1
β-strand	6	1	40
α-helix	7-9	3
β-strand	10-12	3	41
β-strand	17-23	7	40
β-strand	25	1	39
β-strand	32-39	8	42
β-strand	45-52	8	42
β-strand	57-59	3	42
β-strand	65	1	40
β-strand	68-73	6	40
β-strand	78-84	7	40
α-helix	88-90	3
β-strand	92-94	3	41
β-strand	95-101	7	42
β-strand	103	1	43
β-strand	106	1	43
β-strand	116-117	2	42
β-strand	121-125	5	41

Chain I: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	235	1	44
β-strand	240-241	2	45
β-strand	247-253	7	44
α-helix	256-260	5
β-strand	265-270	6	46
β-strand	277-281	5	46
β-strand	285-286	2	46
α-helix	287	1
β-strand	297-299	3	44
β-strand	302-308	7	44
β-strand	317-324	8	46
β-strand	328-331	4	46
β-strand	336	1	46
β-strand	337-338	2	45

4 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	Q9IWR0
DH270.3 variable heavy chain	C, H, M	protein	126	Homo sapiens
DH270.3 variable light chain	D, I, N	protein	110	Homo sapiens

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

>8SAY_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

>8SAY_2 CH848.10.17 gp41 (chains B, G, L)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGTVWGIKQLQARVLAVERYLRDQQL
LGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQ
QEKNEQDLLALD

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

>8SAY_3 DH270.3 variable heavy chain (chains C, H, M)
QVQLVQSGAELKKPGASVKVSCKASGYTLSDYYVHWLRQAPGQGLEWVAWINPTSGRTIS
PRKFQGRVTMTTDTSMNVAYMELRGLRSDDTAVYFCARGGWISLYVDYSYYPNFDSWGQG
TLVSVS

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

>8SAY_4 DH270.3 variable light chain (chains D, I, N)
QPVLTQPASVSGSPGQSITISCTGSSSDVGSYNLVSWYQQHPGKAPKLMIYEVNKWASGV
SDRFAGSKSGNTASLTISRLQAEDEANYFCSSSTNSATVIFGGGTKLTVL

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
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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