1G9N: HIV-1 YU2 GP120 envelope glycoprotein

HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing antibody 17B. Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Dec 2000.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 4
Atoms: 7,714
Mol. weight: 106.4 kDa
Ligands: NAG
Released: 27 Dec 2000

Explore 1G9N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1G9N contains 22 α-helices and 103 β-strands across 4 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 C: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	12-13	2	10
β-strand	17	1	11
β-strand	26-29	4	8
β-strand	35-39	5	8
β-strand	44-46	3	8
α-helix	52-54	3
β-strand	55-56	2	10
α-helix	59-62	4
β-strand	66	1	11
β-strand	70-71	2	10
α-helix	76-78	3
β-strand	80-82	3	9
β-strand	83-86	4	8
β-strand	89-90	2	8
β-strand	93-98	6	9
β-strand	99-102	4	12
β-strand	107-108	2	13
β-strand	111	1	14
β-strand	114-119	6	12
β-strand	127-129	3	15
β-strand	139-140	2	15
β-strand	143-146	4	12
β-strand	149	1	14
β-strand	156-157	2	16
β-strand	161-162	2	15
β-strand	163	1	17
β-strand	166	1	17
β-strand	172-173	2	16
β-strand	175-176	2	13

Chain G: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	1
α-helix	95-97	3
α-helix	99-110	12
β-strand	120-126	7	2
β-strand	196-201	6	2
β-strand	215	1	3
β-strand	218	1	4
β-strand	223-227	5	5
β-strand	236-239	4	1
β-strand	243-245	3	5
β-strand	247	1	4
α-helix	248-250	3
β-strand	251	1	3
β-strand	256	1	6
β-strand	259-261	3	7
β-strand	271-274	4	7
β-strand	284-297	14	7
β-strand	330-334	5	7
α-helix	335-353	19
β-strand	358-361	4	7
β-strand	367	1	8
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
β-strand	413-417	5	7
β-strand	418-421	4	6
β-strand	423-425	3	2
β-strand	432-434	3	2
α-helix	436-438	3
β-strand	444-456	13	7
β-strand	465-470	6	7
α-helix	476-483	8
β-strand	486-490	5	5

Chain H: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	24
α-helix	7-9	3
β-strand	10	1	25
β-strand	17-25	9	24
α-helix	29-31	3
β-strand	32-39	8	25
β-strand	45-52	8	25
α-helix	53-55	3
β-strand	57-60	4	25
α-helix	62-64	3
β-strand	65	1	24
β-strand	68-73	6	24
β-strand	78-84	7	24
β-strand	92-100	9	25
α-helix	104-106	3
β-strand	117-118	2	25
β-strand	122-124	3	25
β-strand	132	1	26
β-strand	135	1	27
β-strand	138-139	2	28
β-strand	151-155	5	28
β-strand	158	1	27
β-strand	160	1	29
β-strand	161	1	26
β-strand	166-169	4	30
α-helix	170-172	3
β-strand	178	1	28
β-strand	181-185	5	29
β-strand	191-194	4	29
β-strand	195-199	5	28
α-helix	201-203	3
β-strand	209-214	6	30
β-strand	222-226	5	30

Chain L: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	18
β-strand	10-13	4	19
β-strand	18-19	2	18
β-strand	22-24	3	18
β-strand	30	1	20
β-strand	33-38	6	19
β-strand	46-48	3	19
β-strand	54	1	19
α-helix	55	1
β-strand	62-66	5	18
β-strand	68	1	20
β-strand	70-77	8	18
α-helix	80-82	3
β-strand	84-90	7	19
β-strand	99-100	2	19
β-strand	105-108	4	19
α-helix	109	1
β-strand	113	1	21
α-helix	114-115	2
β-strand	117-120	4	22
α-helix	124-129	6
β-strand	132-141	10	22
β-strand	142	1	21
β-strand	146-152	7	23
β-strand	161	1	22
β-strand	175-183	9	22
β-strand	193-200	8	23
β-strand	207-208	2	23
β-strand	211-212	2	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein GP120	G	protein	313	Human immunodeficiency virus 1	P35961
T-cell surface glycoprotein CD4	C	protein	185	Homo sapiens	P01730 (AlphaFold model)
Antibody 17B, light chain	L	protein	214	Homo sapiens
Antibody 17B, heavy chain	H	protein	229	Homo sapiens

Sequence of entity 1 (G), FASTA

>1G9N_1 ENVELOPE GLYCOPROTEIN GP120 (chains G)
GARSEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVIT
QACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLN
GSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGAGHCNLSKTQWENTLEQIAIKLKE
QFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCR
IKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNW
RSELYKYKVVKIE

Sequence of entity 2 (C), FASTA

>1G9N_2 T-CELL SURFACE GLYCOPROTEIN CD4 (chains C)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KASNT

Sequence of entity 3 (L), FASTA

>1G9N_3 ANTIBODY 17B, LIGHT CHAIN (chains L)
ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQKSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 4 (H), FASTA

>1G9N_4 ANTIBODY 17B, HEAVY CHAIN (chains H)
QVQLLESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYRNNGFLKHWGQ
GTLVTVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPQPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	14

Primary citation

Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Kwong, P.D., Wyatt, R., Majeed, S. et al. Structure (2000) 8:1329-1339. DOI 10.1016/S0969-2126(00)00547-5 · 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…

Browse structure collections

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