8SAW: DH270.UCA.G57R-CH848.10.17DT

CryoEM structure of DH270.UCA.G57R-CH848.10.17DT. 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: 19,743
Mol. weight: 288.58 kDa
Released: 19 Apr 2023

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

Secondary structure: helices and β-sheets

8SAW contains 51 α-helices and 213 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.

Chains A and E: 7 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	1
β-strand	45-47	3	2
β-strand	53-56	4	3
β-strand	66-67	2	4
β-strand	75-76	2	3
β-strand	84-86	3	2
β-strand	91-92	2	5
α-helix	99-115	17
β-strand	129-132	4	6
β-strand	154-162	9	6
β-strand	169-177	9	6
α-helix	178-180	3
β-strand	181-183	3	6
β-strand	190-193	4	6
β-strand	202-203	2	7
α-helix	204-205	2
β-strand	208-209	2	4
β-strand	215	1	8
β-strand	216-218	3	3
β-strand	223-228	6	2
β-strand	238-239	2	5
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	8
β-strand	259-261	3	9
β-strand	271-273	3	9
β-strand	284-298	15	9
β-strand	302-304	3	6
β-strand	307-308	2	10
β-strand	316-317	2	10
β-strand	320-323	4	6
β-strand	330-334	5	9
α-helix	335-349	15
β-strand	359-361	3	11
α-helix	369-372	4
β-strand	374-378	5	12
β-strand	381-385	5	12
β-strand	393-396	3	11
β-strand	413-417	5	9
β-strand	418-421	4	12
β-strand	423-424	2	7
β-strand	434-435	2	7
α-helix	436-438	3
β-strand	443-455	13	9
β-strand	467-468	2	11
β-strand	469-470	2	9
α-helix	476-480	5
β-strand	486-491	6	2
β-strand	495-499	5	1

Chains B and F: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-541	5
α-helix	573-594	22
β-strand	603-609	7	1
α-helix	619-621	3
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-663	25

Chains C, H and M: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	13
β-strand	9-11	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	32-39	8	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	65	1	13
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-101	10	14
β-strand	117	1	14
β-strand	121-124	4	14

Chains D and N: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	15
β-strand	5	1	16
β-strand	10-12	3	17
β-strand	17-23	7	16
β-strand	35-40	6	18
β-strand	47-50	4	18
β-strand	51	1	19
β-strand	55	1	19
β-strand	64	1	16
β-strand	69	1	16
β-strand	72-78	7	16
α-helix	82-84	3
β-strand	87-95	9	18
β-strand	98-100	3	18
β-strand	102	1	15
β-strand	105-106	2	18
β-strand	107-109	3	17

Chain I: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	34
β-strand	36	1	35
β-strand	41-43	3	36
β-strand	48-54	7	35
β-strand	66-71	6	37
β-strand	78-81	4	37
β-strand	82	1	38
β-strand	86	1	38
β-strand	95	1	35
β-strand	100	1	35
β-strand	103-109	7	35
α-helix	113-115	3
β-strand	118-126	9	37
β-strand	129-131	3	37
β-strand	136	1	34
β-strand	139-140	2	37
β-strand	141-143	3	36

Chain K: 7 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	39
β-strand	14-16	3	40
β-strand	22-25	4	41
β-strand	35-36	2	42
β-strand	44-45	2	41
β-strand	53-55	3	40
β-strand	60-61	2	43
α-helix	68-84	17
β-strand	98-101	4	44
β-strand	113-121	9	44
β-strand	128-136	9	44
α-helix	137-139	3
β-strand	140-142	3	44
β-strand	151-154	4	44
β-strand	163-164	2	45
α-helix	165-166	2
β-strand	169-170	2	42
β-strand	176	1	46
β-strand	177-179	3	41
β-strand	184-189	6	40
β-strand	199-200	2	43
β-strand	203-206	4	40
β-strand	208	1	41
β-strand	212	1	46
β-strand	220-222	3	47
β-strand	232-234	3	47
β-strand	245-259	15	47
β-strand	263-265	3	44
β-strand	268-269	2	48
β-strand	275-276	2	48
β-strand	279-282	4	44
β-strand	290-294	5	47
α-helix	295-309	15
β-strand	318-320	3	49
α-helix	328-331	4
β-strand	333-337	5	50
β-strand	340-344	5	50
β-strand	352-354	3	49
β-strand	370-374	5	47
β-strand	375-378	4	50
β-strand	380-381	2	45
β-strand	391-392	2	45
α-helix	393-395	3
β-strand	400-412	13	47
β-strand	424-425	2	49
β-strand	426-427	2	47
α-helix	433-437	5
β-strand	443-448	6	40
β-strand	452-456	5	39

Chain L: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	26-30	5
α-helix	41-62	22
β-strand	71-77	7	39
α-helix	87-89	3
α-helix	96-103	8
α-helix	104-106	3
α-helix	107-131	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CH848.3.D0949.10.17chim.6R.SOSIP.664 gp120A	A, E, K	protein	471	HIV-1 06TG.HT008	A0A1W6IPB2
CH848.3.D0949.10.17chim.6R.SOSIP.664 gp41	B, F, L	protein	132	HIV-1 06TG.HT008	Q9IWR0
DH270.UCA. G57R heavy chain	C, H, M	protein	127	Homo sapiens	A0A5C2GD27 (AlphaFold model)
DH270.UCA. G57R light chain	D, I, N	protein	110	Homo sapiens	A0A5C2G1R5 (AlphaFold model)

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

>8SAW_1 CH848.3.D0949.10.17chim.6R.SOSIP.664 gp120A (chains A, E, K)
AENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNVWATHACVPTDPSPQELVLGNVT
ENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLICSNATVKNGTVEEMKNCSFN
TTTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINCNTSACTQACPKVTFEPIPIHYC
APAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENLT
NNAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFYATGDIIGDIKQAHCNISEEKWN
DTLQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSFNCGGEFFYCNTSNLFNGTYNGTYI
STNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIAGNITCRSNITGLLLTRDGGTNS
NETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

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

>8SAW_2 CH848.3.D0949.10.17chim.6R.SOSIP.664 gp41 (chains B, F, L)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGTVWGIKQLQARVLAVERYLRDQQL
LGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQ
QEKNEQDLLALD

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

>8SAW_3 DH270.UCA. G57R heavy chain (chains C, H, M)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGRTNY
AQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGGWISLYYDSSGYPNFDYWGQG
TLVTVSS

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

>8SAW_4 DH270.UCA. G57R light chain (chains D, I, N)
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEVSKRPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSSTVIFGGGTKLTVL

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
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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