4LAJ: HIV-1 YU2 envelope gp120 glycoprotein

Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4. Determined by X-ray diffraction at 2.14 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 2.14 Å
Organisms: Human immunodeficiency virus 1, Lama glama
Chains: 12
Atoms: 16,384
Mol. weight: 243.36 kDa
Ligands: NAG, ACA
Released: 14 Aug 2013

Explore 4LAJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LAJ contains 62 α-helices and 176 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: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	15
β-strand	53-56	4	16
β-strand	62	1	17
α-helix	65-73	9
β-strand	75-76	2	16
α-helix	77-78	2
β-strand	84-86	3	15
β-strand	91-94	4	18
α-helix	99-115	17
β-strand	120-123	4	19
β-strand	199-202	4	19
β-strand	207	1	20
β-strand	215	1	21
β-strand	216-218	3	16
β-strand	223-228	6	15
β-strand	236-239	4	18
β-strand	242-245	4	15
β-strand	247	1	16
α-helix	248-250	3
β-strand	251	1	21
β-strand	256	1	22
β-strand	259-261	3	22
α-helix	264-266	3
β-strand	271-273	3	22
α-helix	283	1
β-strand	284-298	15	22
β-strand	328-333	6	22
α-helix	335-353	19
α-helix	357	1
β-strand	358-361	4	22
β-strand	367	1	23
α-helix	369-372	4
β-strand	374-378	5	22
β-strand	381-385	5	22
β-strand	393	1	22
α-helix	395-399	5
β-strand	414-421	8	22
β-strand	423-425	3	19
β-strand	432-434	3	19
α-helix	436-439	4
β-strand	443-456	14	22
β-strand	465-470	6	22
α-helix	475-483	9
β-strand	486-490	5	15

Chain B: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	24
β-strand	53-56	4	25
β-strand	62	1	20
α-helix	65-73	9
β-strand	75-76	2	25
α-helix	77-78	2
β-strand	83-86	4	24
β-strand	91-94	4	26
α-helix	99-115	17
β-strand	120-123	4	27
β-strand	199-202	4	27
β-strand	207	1	17
β-strand	215	1	28
β-strand	216-218	3	25
β-strand	223-228	6	24
β-strand	236-239	4	26
β-strand	242-245	4	24
β-strand	247	1	25
α-helix	248-250	3
β-strand	251	1	28
β-strand	256	1	29
β-strand	259-261	3	29
α-helix	264-266	3
β-strand	271-273	3	29
α-helix	283	1
β-strand	284-298	15	29
β-strand	328-334	7	29
α-helix	335-353	19
α-helix	357	1
β-strand	358-361	4	29
β-strand	367	1	30
α-helix	369-372	4
β-strand	374-378	5	29
β-strand	381-385	5	29
α-helix	388-390	3
β-strand	393-394	2	29
β-strand	413-421	9	29
β-strand	423-425	3	27
β-strand	432-434	3	27
α-helix	436-439	4
β-strand	443-456	14	29
β-strand	465-470	6	29
α-helix	475-483	9
β-strand	486-490	5	24

Chains C, G and K: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
β-strand	17-20	4	30
β-strand	23-26	4	30

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	17-20	4	23
β-strand	23-26	4	23

Chain F: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	8
β-strand	53-56	4	9
α-helix	65-73	9
β-strand	75-76	2	9
α-helix	77-78	2
β-strand	83-85	3	8
β-strand	91-94	4	10
α-helix	99-115	17
β-strand	120-123	4	11
β-strand	199-202	4	11
β-strand	215	1	12
β-strand	216-218	3	9
β-strand	223-228	6	8
β-strand	236-239	4	10
β-strand	242-245	4	8
β-strand	247	1	9
α-helix	248-250	3
β-strand	251	1	12
β-strand	256	1	13
β-strand	259-261	3	13
α-helix	264-266	3
β-strand	271-273	3	13
α-helix	283	1
β-strand	284-298	15	13
β-strand	328-334	7	13
α-helix	335-353	19
α-helix	357	1
β-strand	358-361	4	13
β-strand	367	1	14
α-helix	369-372	4
β-strand	374-378	5	13
β-strand	381-385	5	13
β-strand	413-421	9	13
β-strand	423-425	3	11
β-strand	432-434	3	11
α-helix	436-439	4
β-strand	443-456	14	13
β-strand	465-470	6	13
α-helix	475-483	9
β-strand	486-490	5	8

Chain H: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	31
β-strand	10-12	3	32
β-strand	18-25	8	31
α-helix	29-31	3
β-strand	33-39	7	32
β-strand	46-52	7	32
β-strand	57-60	4	32
α-helix	62-64	3
β-strand	68-73	6	31
β-strand	78-83	6	31
α-helix	88-90	3
β-strand	92-98	7	32
α-helix	108-110	3
β-strand	114	1	32
β-strand	118-122	5	32

Chain I: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	37
β-strand	10-12	3	38
β-strand	18-23	6	37
α-helix	29-31	3
β-strand	33-39	7	38
β-strand	46-52	7	38
β-strand	57-60	4	38
β-strand	65	1	37
β-strand	68-73	6	37
β-strand	78-83	6	37
α-helix	88-90	3
β-strand	92-98	7	38
α-helix	108-110	3
β-strand	114	1	38
β-strand	118-122	5	38

Chain J: 11 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	75-76	2	2
α-helix	77-78	2
β-strand	83-86	4	1
β-strand	91-94	4	3
α-helix	99-115	17
β-strand	120-123	4	4
β-strand	199-202	4	4
β-strand	215	1	5
β-strand	216-218	3	2
β-strand	223-228	6	1
β-strand	236-239	4	3
β-strand	242-245	4	1
β-strand	247	1	2
α-helix	248-250	3
β-strand	251	1	5
β-strand	256	1	6
β-strand	259-261	3	6
α-helix	264-266	3
β-strand	271-274	4	6
α-helix	283	1
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-353	19
α-helix	357	1
β-strand	358-361	4	6
β-strand	367	1	7
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
β-strand	393	1	6
β-strand	413-421	9	6
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	436-439	4
β-strand	443-456	14	6
β-strand	465-470	6	6
α-helix	475-483	9
β-strand	486-490	5	1

2 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 YU2 gp120 envelope glycoprotein	A, B, F, J	protein	376	Human immunodeficiency virus 1	P35961
CD4-mimetic miniprotein M48U1	C, D, G, K	protein	28
Llama single domain antibody, JM4	H, I, L, M	protein	129	Lama glama	A2KD57 (AlphaFold model)

Sequence of entity 1 (A, B, F, J), FASTA

>4LAJ_1 HIV-1 YU2 gp120 envelope glycoprotein (chains A, B, F, J)
MPMGSLQPLATLYLLGMLVASVLAVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDP
NPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEP
IPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVI
RSENFTNNAKTIIVQLNESVVINCTRPNNGGSGSGGDIRQAHCNLSKTQWENTLEQIAIK
LKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITL
PCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMR
DNWRSELYKYKVVKIE

Sequence of entity 2 (C, D, G, K), FASTA

>4LAJ_2 CD4-mimetic miniprotein M48U1 (chains C, D, G, K)
XNLHFCQLRCKSLGLLGRCAPTXCACVX

Sequence of entity 3 (H, I, L, M), FASTA

>4LAJ_3 Llama single domain antibody, JM4 (chains H, I, L, M)
EVQLVESGGGLVQPGGSLRLSCAASGFTLDYYSIGWFRQAPGKEREGVSCISDSDGRTYY
ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATDCTVDPSLLYVMDYYGKGTQVT
VSSAAAEQK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	35
ACA	6-aminohexanoic acid	C6 H13 N O2	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Heavy Chain-Only IgG2b Llama Antibody Effects Near-Pan HIV-1 Neutralization by Recognizing a CD4-Induced Epitope That Includes Elements of Coreceptor- and CD4-Binding Sites. Acharya, P., Luongo, T.S., Georgiev, I.S. et al. J Virol (2013) 87:10173-10181. DOI 10.1128/JVI.01332-13 · PubMed

Other PDB entries of the same protein (UniProt P35961), best resolution first:

4JZZ 1.49 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4JZW 1.78 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4KA2 1.79 Å, Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120
4RWY 2.13 Å, Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC131…
4K0A 2.13 Å, Crystal structure of CD4-mimetic miniprotein M48U7 in complex with HIV-1 YU2 gp120
1YYM 2.2 Å, crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120…
2NY7 2.3 Å, HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing…
2I60 2.4 Å, Crystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, in complex with HIV-1…
4DVR 2.5 Å, Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557
4JO3 2.6 Å, Crystal structure of rabbit mAb R20 Fab in complex with V3 C-terminus of HIV-1 Consensus…
1YYL 2.75 Å, crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2…
1G9N 2.9 Å, HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing…

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