3HI1: HIV-1 gp120

Structure of HIV-1 gp120 (core with V3) in Complex with CD4-Binding-Site Antibody F105. Determined by X-ray diffraction at 2.9 Å resolution. Released 17 Nov 2009.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Human immunodeficiency virus type 1, Homo sapiens
Chains: 6
Atoms: 11,670
Mol. weight: 172.58 kDa
Ligands: NAG
Released: 17 Nov 2009

Explore 3HI1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3HI1 contains 53 α-helices and 135 β-strands across 6 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: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	25
β-strand	10-14	5	26
β-strand	19-28	11	25
α-helix	30-32	3
β-strand	33-38	6	26
β-strand	45-49	5	26
β-strand	53-54	2	26
α-helix	55	1
β-strand	62-75	14	25
α-helix	80-82	3
β-strand	84-92	9	26
β-strand	95-98	4	26
β-strand	102-107	6	26
β-strand	111	1	27
α-helix	112-113	2
β-strand	114-118	5	28
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	28
β-strand	140	1	27
β-strand	144-150	7	29
β-strand	153-154	2	29
α-helix	155	1
β-strand	159-163	5	28
α-helix	164-167	4
β-strand	173-182	10	28
α-helix	183-186	4
β-strand	191-198	8	29
β-strand	205-210	6	29

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	30
β-strand	11-12	2	31
β-strand	18-25	8	30
β-strand	33-39	7	32
β-strand	45-52	8	32
β-strand	57-59	3	32
α-helix	64-66	3
β-strand	67-72	6	30
α-helix	73-75	3
β-strand	77-82	6	30
α-helix	84-86	3
β-strand	88-94	7	32
β-strand	101-103	3	32
β-strand	107-109	3	32
β-strand	110-111	2	31
α-helix	115-116	2
β-strand	117	1	33
β-strand	120-124	5	34
α-helix	125-127	3
β-strand	135-145	11	34
β-strand	146	1	33
β-strand	151-154	4	35
α-helix	155-157	3
β-strand	159	1	35
β-strand	163-165	3	34
α-helix	166-168	3
β-strand	169-170	2	34
β-strand	176-185	10	34
α-helix	186-190	5
β-strand	194-200	7	35
α-helix	201-203	3
β-strand	205-211	7	35

Chain G: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	1
α-helix	99-114	16
α-helix	119-122	4
β-strand	205-208	4	2
β-strand	215-218	4	3
α-helix	219-220	2
β-strand	223-228	6	4
β-strand	236-239	4	1
β-strand	242-245	4	4
β-strand	247	1	3
α-helix	248-250	3
β-strand	251	1	3
β-strand	256	1	5
β-strand	259-261	3	6
α-helix	264-266	3
β-strand	271-274	4	6
β-strand	284-297	14	6
β-strand	330-334	5	6
α-helix	335-353	19
β-strand	358-361	4	7
β-strand	366	1	8
α-helix	369-372	4
β-strand	374-377	4	5
β-strand	382-385	4	5
α-helix	388-390	3
β-strand	393	1	7
β-strand	413-417	5	6
β-strand	418-421	4	5
β-strand	444	1	6
β-strand	447-454	8	6
β-strand	455-456	2	7
β-strand	465-469	5	7
α-helix	476-483	8
β-strand	486-490	5	4

Chain H: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	14
β-strand	11-12	2	15
β-strand	18-25	8	14
β-strand	27	1	8
β-strand	33-39	7	16
β-strand	45-52	8	16
β-strand	57-59	3	16
α-helix	64-66	3
β-strand	67-72	6	14
α-helix	73-75	3
β-strand	77-82	6	14
α-helix	84-86	3
β-strand	88-94	7	16
β-strand	101-103	3	16
β-strand	107-109	3	16
β-strand	110-111	2	15
α-helix	115-116	2
β-strand	117	1	17
β-strand	120-124	5	18
α-helix	125-127	3
β-strand	135-145	11	18
β-strand	146	1	17
β-strand	151-154	4	19
α-helix	155-157	3
β-strand	159	1	19
β-strand	163-165	3	18
α-helix	166-168	3
β-strand	169-170	2	18
β-strand	176-185	10	18
α-helix	186-190	5
β-strand	194-200	7	19
α-helix	201-203	3
β-strand	205-211	7	19

Chain J: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	20
α-helix	99-114	16
α-helix	118-122	5
β-strand	205-208	4	3
β-strand	215-218	4	2
α-helix	219-220	2
β-strand	223-228	6	21
β-strand	236-239	4	20
β-strand	242-245	4	21
β-strand	247	1	2
α-helix	248-250	3
β-strand	251	1	2
β-strand	256	1	22
β-strand	259-261	3	23
α-helix	264-266	3
β-strand	271-274	4	23
β-strand	284-296	13	23
β-strand	330-333	4	23
α-helix	335-353	19
β-strand	358-361	4	24
α-helix	369-372	4
β-strand	374-377	4	22
β-strand	381-385	5	22
α-helix	388-390	3
β-strand	393	1	24
β-strand	414-417	4	23
β-strand	418-422	5	22
β-strand	447-454	8	23
β-strand	455-456	2	24
β-strand	465-469	5	24
α-helix	476-483	8
β-strand	486-490	5	21

Chain L: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	9
β-strand	10-14	5	10
β-strand	19-28	11	9
α-helix	30-32	3
β-strand	33-38	6	10
β-strand	45-49	5	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-75	14	9
β-strand	84-92	9	10
β-strand	95-98	4	10
β-strand	102-107	6	10
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	144-150	7	13
β-strand	153-154	2	13
α-helix	155	1
β-strand	159-163	5	12
α-helix	164-167	4
β-strand	173-182	10	12
α-helix	183-186	4
β-strand	191-198	8	13
β-strand	205-210	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein 120	G, J	protein	321	Human immunodeficiency virus type 1	P35961
F105 Light Chain	A, L	protein	215	Homo sapiens	Q6PIL8 (AlphaFold model)
F105 Heavy Chain	B, H	protein	225	Homo sapiens

Sequence of entity 1 (G, J), FASTA

>3HI1_1 Glycoprotein 120 (chains G, J)
TENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAG
FAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAK
TIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLE
QIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTG
RNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPG
GGDMRDNWRSELYKYKVVKIE

Sequence of entity 2 (A, L), FASTA

>3HI1_2 F105 Light Chain (chains A, L)
EIVLTQSPGTLSLSAGERATLSCRASQSVSSRYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRVEPEDFAVYYCQQYDNSVCTFGQGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B, H), FASTA

>3HI1_3 F105 Heavy Chain (chains B, H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISSHYWSWIRQSPGKGLQWIGYIYYSGSTNYS
PSLKSRVTISVETAKNQFSLKLTSMTAADTAVYYCARGPVPAVFYGDYRLDPWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Ligands and cofactors

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

Primary citation

Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120. Chen, L., Do Kwon, Y., Zhou, T. et al. Science (2009) 326:1123-1127. DOI 10.1126/science.1175868 · 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
4LAJ 2.14 Å, Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic…
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…

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