9AUH: CH848.d949.10.17.GS-DH270.UCA3

Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3. Determined by electron microscopy at 3.6 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,312
Mol. weight: 368.81 kDa
Ligands: NAG
Released: 5 Feb 2025

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

Secondary structure: helices and β-sheets

9AUH contains 64 α-helices and 210 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, 46 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	60-62	3
β-strand	68	1	4
β-strand	75-76	2	3
α-helix	77-78	2
β-strand	84-85	2	2
β-strand	91-93	3	5
α-helix	99-114	16
β-strand	121	1	6
α-helix	128	1
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	181-182	2	10
β-strand	190-191	2	7
β-strand	192-193	2	10
β-strand	202	1	6
β-strand	203	1	11
α-helix	204-205	2
β-strand	209	1	4
β-strand	215	1	12
β-strand	216-218	3	3
β-strand	221	1	2
β-strand	223-228	6	2
β-strand	237-239	3	5
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	12
α-helix	264-266	3
β-strand	271-273	3	13
β-strand	284-287	4	13
β-strand	294-297	4	14
β-strand	304-309	6	15
β-strand	315-320	6	15
β-strand	329-334	6	14
α-helix	335-349	15
β-strand	357-361	4	13
β-strand	374-378	5	14
β-strand	381-385	5	14
β-strand	394-395	2	13
β-strand	413-421	9	14
β-strand	423	1	11
β-strand	435	1	11
α-helix	436-438	3
β-strand	445-447	3	14
β-strand	451-456	6	13
β-strand	465-470	6	13
α-helix	476-482	7
β-strand	486-491	6	2
β-strand	494-499	6	1

Chain B: 11 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	16
β-strand	45-47	3	17
β-strand	55-56	2	18
α-helix	58-60	3
α-helix	74	1
β-strand	75-76	2	18
α-helix	77-78	2
β-strand	83-85	3	17
β-strand	91-94	4	19
α-helix	99-115	17
α-helix	128	1
β-strand	129-130	2	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	190-191	2	20
β-strand	192-193	2	23
β-strand	202-203	2	24
α-helix	204-205	2
β-strand	215	1	25
β-strand	216	1	18
β-strand	218	1	26
α-helix	219-220	2
β-strand	223-228	6	17
β-strand	236-239	4	19
β-strand	242-245	4	17
β-strand	247	1	26
β-strand	251	1	25
β-strand	271-273	3	27
β-strand	285-287	3	27
β-strand	293-296	4	28
β-strand	304-309	6	29
β-strand	315-320	6	29
β-strand	330-334	5	28
α-helix	335-349	15
β-strand	357-361	4	30
β-strand	374-378	5	31
β-strand	381-385	5	31
β-strand	393-395	3	30
β-strand	413-417	5	28
β-strand	418-419	2	31
β-strand	423-424	2	24
β-strand	434-435	2	24
α-helix	436-438	3
β-strand	447-448	2	28
β-strand	451-453	3	27
β-strand	454-456	3	30
β-strand	465-470	6	30
α-helix	476-482	7
β-strand	486-491	6	17
β-strand	494-499	6	16

Chain C: 11 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	32
β-strand	45-47	3	33
α-helix	52	1
β-strand	53-56	4	34
α-helix	58-60	3
β-strand	75-76	2	34
β-strand	84-85	2	33
β-strand	91-93	3	35
α-helix	99-115	17
α-helix	123-125	3
β-strand	129	1	36
β-strand	130	1	37
β-strand	133	1	38
α-helix	135-137	3
β-strand	154-155	2	38
β-strand	158	1	37
β-strand	159-162	4	39
β-strand	169-172	4	39
β-strand	176-177	2	38
β-strand	181-183	3	36
β-strand	191-193	3	36
α-helix	194-196	3
β-strand	203	1	40
β-strand	215	1	41
β-strand	216-218	3	34
β-strand	223-228	6	33
β-strand	237-239	3	35
β-strand	242-245	4	33
β-strand	247	1	34
β-strand	251	1	41
β-strand	259-260	2	42
α-helix	264-266	3
β-strand	271-273	3	42
β-strand	284-297	14	42
β-strand	304-307	4	43
β-strand	317-320	4	43
β-strand	330-334	5	42
α-helix	335-349	15
β-strand	357-361	4	42
α-helix	369-372	4
β-strand	374-378	5	44
β-strand	381-385	5	44
β-strand	393-395	3	42
β-strand	413-417	5	42
β-strand	418-421	4	44
β-strand	423-424	2	40
β-strand	434-435	2	40
α-helix	436-438	3
β-strand	444-456	13	42
β-strand	465-470	6	42
α-helix	476-482	7
β-strand	486-491	6	33
β-strand	494-498	5	32

Chain D: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	513-515	3
α-helix	531-534	4
α-helix	537-540	4
α-helix	573-595	23
β-strand	603-609	7	1
α-helix	619-625	7
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-663	25

Chain E: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-541	5
α-helix	574-595	22
β-strand	603-609	7	16
α-helix	610-611	2
α-helix	619-625	7
α-helix	628-635	8
α-helix	640-663	24

Chain F: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	538-542	5
α-helix	571-595	25
β-strand	603-609	7	32
α-helix	619-624	6
α-helix	628-635	8
α-helix	640-663	24

Chain G: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	45
β-strand	10-12	3	46
β-strand	18-25	8	45
α-helix	29-31	3
β-strand	32-39	8	46
β-strand	46-51	6	46
β-strand	58	1	46
β-strand	68-73	6	45
β-strand	78-83	6	45
α-helix	88-90	3
β-strand	92-101	10	46
β-strand	117	1	46
β-strand	121-125	5	46

Chain H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	47
β-strand	10-12	3	48
β-strand	18-25	8	47
α-helix	29-31	3
β-strand	32-39	8	48
β-strand	45-51	7	48
β-strand	58	1	48
β-strand	68-69	2	47
β-strand	72-73	2	47
β-strand	78-83	6	47
α-helix	88-90	3
β-strand	92-101	10	48
β-strand	117	1	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 heavy chain	G, H, I	protein	232	Homo sapiens
UCA3 light chain	J, K, L	protein	216	Homo sapiens

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

>9AUH_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

>9AUH_2 HIV-1 BG505 DS-SOSIP glycoprotein gp41 (chains D, E, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>9AUH_3 UCA3 heavy chain (chains G, H, I)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNY
AQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGGWISLYYDSSGYPNFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

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

>9AUH_4 UCA3 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	30

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
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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