9AUG: CH848.d949.10.17.GS-DH270.UCA3.G57R

Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R. Determined by electron microscopy at 3.8 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,211
Mol. weight: 369.56 kDa
Ligands: NAG
Released: 5 Feb 2025

Explore 9AUG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AUG contains 64 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: 13 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-46	2	2
β-strand	55-56	2	3
α-helix	58-61	4
β-strand	67	1	4
β-strand	75-76	2	3
α-helix	77-78	2
β-strand	83-85	3	2
β-strand	91-94	4	5
α-helix	100-115	16
α-helix	120	1
β-strand	121	1	6
α-helix	123-125	3
β-strand	129-130	2	7
β-strand	154-155	2	8
β-strand	158	1	7
β-strand	159-162	4	9
β-strand	169-172	4	9
β-strand	176-177	2	8
α-helix	178-180	3
β-strand	181-183	3	7
β-strand	190-193	4	7
β-strand	202-203	2	6
α-helix	204-205	2
β-strand	209	1	4
β-strand	215-216	2	3
β-strand	218	1	10
β-strand	223-228	6	2
β-strand	236-239	4	5
β-strand	242-245	4	2
β-strand	247	1	10
β-strand	251	1	3
β-strand	260	1	11
β-strand	271-273	3	11
β-strand	284-287	4	11
β-strand	293-296	4	12
β-strand	304-308	5	13
β-strand	316-320	5	13
β-strand	330-334	5	12
α-helix	335-349	15
β-strand	357-361	4	11
α-helix	369-372	4
β-strand	373-378	6	14
β-strand	381-386	6	14
β-strand	393-395	3	11
α-helix	406-408	3
β-strand	413-417	5	12
β-strand	418-421	4	14
β-strand	423-424	2	6
α-helix	426-428	3
β-strand	434-435	2	6
α-helix	436-438	3
β-strand	447-448	2	12
β-strand	451-456	6	11
β-strand	465-470	6	11
α-helix	476-482	7
β-strand	487-491	5	2
β-strand	494-499	6	1

Chain B: 12 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-46	12	15
β-strand	56	1	16
α-helix	58-60	3
α-helix	75	1
β-strand	76	1	16
β-strand	84-85	2	15
β-strand	91-94	4	17
α-helix	100-113	14
β-strand	121	1	18
α-helix	128	1
β-strand	129	1	19
β-strand	130	1	20
β-strand	154-155	2	21
β-strand	158	1	20
β-strand	159-162	4	22
β-strand	169-172	4	22
β-strand	176-177	2	21
α-helix	178-180	3
β-strand	181-182	2	23
β-strand	191	1	19
β-strand	192-193	2	23
β-strand	202	1	18
α-helix	203-205	3
β-strand	215	1	24
β-strand	218	1	25
β-strand	223-228	6	15
β-strand	236-239	4	17
β-strand	242-245	4	15
β-strand	247	1	25
β-strand	251	1	24
β-strand	259	1	26
β-strand	271-273	3	26
β-strand	284-287	4	26
β-strand	294-296	3	27
β-strand	304-308	5	28
β-strand	316-320	5	28
β-strand	329-334	6	27
α-helix	335-349	15
β-strand	357-361	4	29
α-helix	369-372	4
β-strand	374-378	5	27
β-strand	381-385	5	27
β-strand	393-395	3	29
α-helix	407-411	4
β-strand	413-419	7	27
α-helix	436-438	3
β-strand	447	1	27
β-strand	451-456	6	26
α-helix	457-458	2
β-strand	465-467	3	29
β-strand	468-470	3	26
α-helix	476-481	6
β-strand	486-499	14	15

Chain C: 12 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-46	12	30
β-strand	55-56	2	31
α-helix	58-61	4
β-strand	75-76	2	31
α-helix	77-78	2
β-strand	83-85	3	30
β-strand	91-94	4	32
α-helix	99-114	16
β-strand	121	1	33
β-strand	129-130	2	34
β-strand	154-155	2	35
β-strand	158	1	34
β-strand	159-162	4	36
β-strand	169-172	4	36
β-strand	176-177	2	35
α-helix	178-180	3
β-strand	181-182	2	37
β-strand	190-191	2	34
β-strand	192-193	2	37
α-helix	194-196	3
β-strand	202-203	2	33
α-helix	204-205	2
β-strand	215	1	38
β-strand	216	1	31
β-strand	218	1	39
β-strand	223-228	6	30
β-strand	236-239	4	32
β-strand	242-245	4	30
β-strand	247	1	39
β-strand	251	1	38
β-strand	259-260	2	40
β-strand	271-273	3	40
α-helix	283	1
β-strand	284-287	4	40
β-strand	293-296	4	41
β-strand	304-308	5	42
β-strand	316-320	5	42
β-strand	329-334	6	41
α-helix	335-349	15
β-strand	357-361	4	40
α-helix	369-372	4
β-strand	374-378	5	43
β-strand	381-385	5	43
β-strand	393-395	3	40
β-strand	413-418	6	41
β-strand	419	1	43
β-strand	423-424	2	33
α-helix	426-428	3
β-strand	434-435	2	33
α-helix	436-438	3
β-strand	447-448	2	41
β-strand	451-456	6	40
β-strand	465-470	6	40
α-helix	476-482	7
β-strand	486-499	14	30

Chain D: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	532-534	3
α-helix	538-541	4
α-helix	542-544	3
α-helix	570-595	26
β-strand	603-609	7	1
α-helix	619-625	7
α-helix	628-635	8
α-helix	639-663	25

Chain E: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	533-535	3
α-helix	539-542	4
α-helix	574-594	21
β-strand	603-609	7	15
α-helix	619-625	7
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-663	25

Chain F: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	537-540	4
α-helix	573-595	23
β-strand	604-609	6	30
α-helix	619-625	7
α-helix	628-635	8
α-helix	636-638	3
α-helix	640-663	24

Chain G: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	44
β-strand	10-12	3	45
β-strand	17-25	9	44
α-helix	29-31	3
β-strand	32-39	8	45
β-strand	41	1	46
β-strand	43	1	46
β-strand	46-51	6	45
β-strand	58-59	2	45
β-strand	68-73	6	44
β-strand	78-84	7	44
α-helix	88-90	3
β-strand	92-101	10	45
β-strand	117	1	45
β-strand	121-125	5	45

Chain H: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	47
β-strand	10-12	3	48
β-strand	17-25	9	47
α-helix	29-31	3
β-strand	32-39	8	48
β-strand	45-51	7	48
β-strand	58-59	2	48
β-strand	68-71	4	47
β-strand	78-84	7	47
α-helix	88-90	3
β-strand	92-101	10	48
β-strand	121-125	5	48

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
HIV-1 BG505 DS-SOSIP glycoprotein gp120	A, B, C	protein	469	Human immunodeficiency virus 1	A0A1W6IPB2
HIV-1 BG505 DS-SOSIP glycoprotein gp41	D, E, F	protein	153	Human immunodeficiency virus 1	D0PUM0
UCA3.G57R heavy chain	G, H, I	protein	232	Homo sapiens
UCA3.G57R light chain	J, K, L	protein	216	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>9AUG_1 HIV-1 BG505 DS-SOSIP glycoprotein gp120 (chains A, B, C)
AENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNVWATHACVPTDPSPQELVLGNVT
ENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLICSDAGSGGVEEMKNCSFNTT
TEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINCNTSACTQACPKVTFEPIPIHYCAP
AGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENLTNN
AKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFYATGDIIGDIKQAHCNISEEKWNDT
LQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSFNCGGEFFYCNTSNLFNGTYNGTYIST
NSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIAGNITCRSNITGLLLTRDGGTNSNE
TETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Sequence of entity 2 (D, E, F), FASTA

>9AUG_2 HIV-1 BG505 DS-SOSIP glycoprotein gp41 (chains D, E, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (G, H, I), FASTA

>9AUG_3 UCA3.G57R heavy chain (chains G, H, I)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGRTNY
AQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGGWISLYYDSSGYPNFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 4 (J, K, L), FASTA

>9AUG_4 UCA3.G57R light chain (chains J, K, L)
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEVSKRPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSSTVIFGGGTKLTVLGQPKANPTVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	27

Primary citation

An engineered immunogen activates diverse HIV broadly neutralizing antibody precursors and promotes acquisition of improbable mutations. Swanson, O.M., Zhang, Q.E., Van Itallie, E. et al. Sci Transl Med (2025) 17:eadr2218-eadr2218. DOI 10.1126/scitranslmed.adr2218 · 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…
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
9AUI 3.8 Å, Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA4

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